83 Ciona intestinalis Cytochrome P450s

This page was revised Jan. 7, 2003. This table provides a comprehensive cross reference table between Ciona intestinalis P450s assembled from individual sequence reads prior to the first genome assembly (sequences assembled up to Oct. 24, 2002), and the P450s assembled in the JGI Ciona assembly version 1.0. The sequence order is the same as seen on the Ciona phylogenetic tree (excluding the Ciona savignyi sequences and seqs 91, 231 and 232 that are not in the tree). The scaffold location of the minus strand sequences are not completely correct, because the numbering on the JGI blast output is backwards for minus strand hits. In addition to that, the 3 prime nucleotide number minus the 5 prime nucleotide number = the number of amino acids, not 3X the number of amino acids. So there are a few problems with the blast numbering. The process of reconciling the JGI assembled sequences with my assembled sequences is not finished yet. There are improvements to be made in both directions, sometimes my assemblies are more accurate, sometimes JGIs are more accurate. The current best estimate is that there are probably 81 functional P450s in Ciona intestinalis. There are two pseudogenes, seqs 91 and 232. Seq 231 is not found in the JGI assembly and it is partial, though it is predicted to be from a full gene based on its strong 80% identity to seq 64. The ci numbers are linked to the JGI entry for that ci#. The sequence can be obtained from that page by clicking on "get sequence". My sequence assemblies can be found in the FASTA file. At a later time I may add a blast comparison between the two assemblies to show where they do not agree. Some sequences occur at the ends of scaffolds and may provide the evidence needed to link scaffolds. For example, sequence 16 has two parts on two different scaffolds. They overlap exactly in exon 6. So these scaffolds should probably be joined. A similar situation is seen in seq 109. Sequence 2 and sequence 4 both run off the end of scaffolds. These two sequences are adjacent on the dendrogram, so the two are probably in a gene cluster and these two scaffolds (27 and 1257) should be adjacent. Sequence 151 has two parts that do not join. However sequence 151 is homologous to a complete sequence from C. savignyi that suggests the two parts (scaffolds 357 and 996) belong to the same gene.

seq#	Scaffold	ci #	strand	aa	exons	Scaffold location	Scaffold size	comments
167	1239	ci0100138987	-	1-490	1-10	3347-7519	11509 bp	complete
166	187	ci0100138282	-	1-497	1-10	52448-56649	158258 bp	complete
169	544	ci0100150360	-	1-512	1-8	30328-34827	45966 bp	complete
164	136	ci0100153637	-	36-509	2-10	177570-181904	232117 bp	exon 1 not detected
180	111	ci0100141900	+	1-432	1-9	40151-43640	260550 bp	complete very odd seq
94	13	ci0100143924	+	1-607	1-9	297502-305021	614915 bp	complete N-term extension
190	13	ci0100143944	-	1-565	1-7	305953-312466	614915 bp	complete
192	5	ci0100143856	-	1-497	1-6	161647-164577	753052 bp	complete
204	83	ci0100151525	-	1-493	1-11	10090-15485	294982 bp	complete
182b	83	ci0100131379	-	1-508	1-11	23537-29791	294982 bp	complete
182a	83	ci0100147340	-	1-508	1-11	17751-22173	294982 bp	complete
136	88	ci0100142705	-	1-497	1-10	99533-105660	292531 bp	complete
186	116	ci0100131439	-	1-490	1-11	37035-41638	253995 bp	complete
46	35	ci0100131189	-	1-526	1-7	240254-243665	458350 bp	complete
15	2	ci0100132188	+	1-531	1-6	115243-117466	919088 bp	complete
25	27	ci0100134415	+	1-607	1-6	357708-364389	480478 bp	complete
49	8	ci0100136792	-	1-531	1-6	484460-488264	681948 bp	complete
40	744	ci0100138492	-	1-471	2-9	2570-7152	26277 bp	exon 1 not detected
184	36	ci0100153789	-	1-515	1-10	186368-193205	429292 bp	complete
222	38	ci0100144128	+	1-498	1-10	186017-190262	397834 bp	complete
17	592	ci0100131843	-	1-519	1-10	25042-34375	40561 bp	complete 4000 bp 1st intron
84	147	ci0100144919	+	1-494	1-10	43217-47457	222906 bp	complete
51	1133	ci0100150675	+	1-488	1-2	9989-11055	14196 bp	complete
198	846	ci0100130969	+	1-466	1-8	15489-19130	21299 bp	complete
41	344	ci0100149995	-	1-494	1-5	15302-17488	80700 bp	complete
6	43	ci0100133889	+	1-504	1-9	120794-123876	362962 bp	complete
39	133	ci0100150103	-	1-505	1-9	26184-29899	227810 bp	complete
21	24	ci0100150103	-	1-494	1-9	319733-322310	493144 bp	complete
7b	37	ci0100139379	-	1-482	1-9	260933-264135	424764 bp	complete
7a	37	ci0100139346	-	1-482	1-9	257757-259491	424764 bp	complete
16	311	ci0100140915	+	1-293	1-6	93294-96689	98311 bp	N-term
16	1266	ci0100137403	+	252-501	6-9	1786-3932	11203 bp	C-term
202	638	ci0100132628	+	1-512	1-9	5561-8704	36007 bp	complete and partial dup. of exon 1
43	638	ci0100132600	+	1-511	1-9	1050-3985	36007 bp	complete
196	39	ci0100152256	-	1-514	1-9	241602-246268	402610 bp	complete
66	174	ci0100133948	+	1-513	1-9	82507-85647	186786 bp	complete
64	36	ci0100152549	+	1-507	1-9	153884-156108	429292 bp	complete
57	36	ci0100152549	+	1-512	1-9	149304-152108	429292 bp	complete
33	230	ci0100137396	-	1-510	1-9	31420-334839	141404 bp	complete
102	1	ci0100151989	-	1-496	1-2, 4-9	884424-887570	972361 bp	missing part of exon 2 and all of exon 3
103	91	ci0100135419	-	1-505	1-9	245271-248731	282773 bp	complete
157	92	ci0100148852	-	1-495	1-9	270432-274571	292709 bp	complete
36	304	ci0100152549	+	1-496	no introns	82343-83830	98326 bp	complete
91	304	no annotation	-	406-493	8-9?	84999-85107	98326 bp	pseudogene
5	350	ci0100141208	-	1-476	1-9	37969-42793	83283 bp	complete
58	144	ci0100144015	+	1-492	1-9	12831-16538	209353 bp	complete
14	144	ci0100132260	-	1-252	1-5	496-2939	209353 bp	runs off end
31	11	ci0100147352	-	1-214, 260-504	1-4, 6-9	652191-655868	658104 bp	missing exon 5
55	106	ci0100138298	-	1-494	1-9	201061-206406	267246 bp	complete
48	106	ci0100130435	+	1-497	1-9	196663-199901	267246 bp	complete
4	1257	ci0100135981	-	1-172	1-4	164-851	13567 bp	runs off end
27	1257	ci0100136000	+	1-497	1-9	2678-6033	13567 bp	complete
1	1257	ci0100131008	+	1-188, 250-393	1-3.5, 6-8	7055-9749	13567 bp	assembly problems probably one gene
1	1257	ci0100131008	+	112-338, 394-497	1.5-7, 9	9992-12062	13567 bp	assembly problems probably one gene
209	324	ci0100147330	+	1-496	1-9	1628-4892	90072 bp	complete
72	817	ci0100136116	+	1-488	1-9	3188-9799	24028 bp	complete 2 copies of exon 2
106	149	ci0100153482	-	1-504	1-10	36996-39661	222761 bp	complete
18	149	ci0100137673	+	1-504	1-10	41196-43841	222761 bp	complete
20	54	ci0100147280	+	1-494	1-10	16357-20237	349210 bp	complete
2	27	ci0100144992	+	429-497	9	1-102	480478 bp	runs off end
208	19	ci0100139081	-	1-452	2-13	350362-356610	548072 bp	cannot ID exon 1
62	918	ci0100151040	+	1-481	1-5	8336-10725	18933 bp	complete, part of exon 5 dup. after gene end
26	48	ci0100154611	+	1-492	no introns	49424-49923	393431 bp	complete
42	3	ci0100139255	+	27-537	1-5	1-2600	866863 bp	missing 1-26 of exon 1 runs off end
29	12	ci0100145514	+	1-502	1-4	327602-329890	625398 bp	complete
65	12	ci0100145536	+	1-501	1-5	331861-333829	625398 bp	complete is last exon split?
34	63	ci0100152358	+	1-503	1-4	209228-211408	354958 bp	complete
232	41	no annotation	-	1-61, 356-509	1-2, 11-14	2948-6288	406245 bp	pseudogene
119	41	no annotation	-	1-61	1-2	7-1002	406245 bp	N-term
119	75	ci0100140050	+	62-509	2-14	2106-8270	316770 bp	join scaffold 41 runs off end
112	75	ci0100140585	+	1-509	1-14	8925-16463	316770 bp	complete
125	75	ci0100151443	+	1-508	1-14	17342-24230	316770 bp	complete
118	262	ci0100133019	+	1-512	no introns	77325-77874	115427 bp	complete
129	8	ci0100135592	-	1-546	1-11	3701-8421	661948 bp	complete
109	8	ci0100134523	-	1-324	1-6	122-2467	661948 bp	N-term half
109	359	ci0100151551	-	460-546	10-11	78497-78920	79400 bp	C-term
159	359	ci0100150610	-	1-536	1-11	68718-75613	79400 bp	complete
158	176	ci0100138987	+	1-547	1-11	192129-196437	197985 bp	complete
151	357	ci0100151682	-	1-211	1-4	224-2360	81286 bp	N-term runs off end
151	996	ci0100147473	+	241-430	8-11	402-2256	16667 bp	C-term runs off end
148	100	ci0100144682	-	1-486, gap	1-6, 8-11	151778-156514	276848 bp	missing exon 7
147	78	ci0100152205	+	1-536	1-11	136637-140140	307118 bp	complete
145	81	ci0100143467	+	1-501	1-11	198977-206748	303162 bp	complete
155	21	ci0100151100	+	1-513	1-12	370383-375609	531011 bp	complete
110	21	ci0100151041	+	1-512	1-12	364082-369116	531011 bp	complete
115	15	ci0100146084	+	1-503	1-3	381100-382367	591421 bp	complete
134	46	ci0100142368	-	1-503	1-3	116988-118566	393349 bp	complete

Sequence 231 is not found in the JGI assembly v1.0. It may be located in the gap upstream of scaffold 638, since there is a related gene (seq 43) at the end of this scaffold and it is already part of a P450 gene cluster with sequence 202.