RetrogeneDB ID: retro_csav_26

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_48:2684045..2684873(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000010900
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSA.5848
• Ensembl ID: ENSCSAVG00000000472
• Aliases: None
• Description: None

Sequence

>retro_csav_26
TCTGGCTCCGAGGAAGAACAGTCTAGAAAGTTATTTGTTGGTGGCCTAAACCACGATACCACCGATGATGGAATGCGGGA
ATATTTTGCAAAGTACGGGAATATTACCGATTGCGTGGTGATCAGAGAACAGGGAACCGACCGCTCGAAAGGATTTGGGT
TCGTTACCTTTGAAACCGAGGTGGAAGCAGATGCGTGTATGGATGAACGACCTCATGTTCTTGATACAAGAAAAATCGAC
GTGAAACGGGCCGTTTCCCGAGAAGAGTCGTCCAAACCAGGTGCTCATACTCAGGTGAAAAAGATATTTGTTGGAGGTGT
TAAAGAGGGTTGCGATGAGCAGACCTTGAGAGAATACTTTGATAGTTTTTCAAAGAGGTCACTTATACAGTCGGTGGAAA
TACCATTGGAACGGGATACACAGCGTCCAAAGGGCTTTGCGTTTGTAACCTTTGAAGACTTTGACATTGTTGATAAGTTA
GTGGCACGAAGGCATCACGATATTGCTGGGTTTAAATGCCAAGTGAAGAAAGCTCTTTCAAAGCAGGAGATGGAACGTTC
GAAACAAGAACTGGAAACCAAGCAACGATGGTCAGGCAGCAGGGGTGGAACTGGAAAGGGGGATTACCAATATGGTGGTT
ATGGTGGTTACGAAGGACAGGGTCATGGGAATTACCGTCCAATGAGGGGTCAATATGGACAAAGATCTAGTGGTCCATAT
GGGGGTGGGTACGGTAGGGGTGGCTCAAGTAGTGGATATGGGAGTAGGGGTGGTGGCGGTGGAGGTTATGGGGGTAGGGG
AGGAGGGTATAGCAAAAGAGGTGGCGGT

Alignment

ORF - retro_csav_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.89 %
• Parental protein coverage: 98.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGSEEEQLRKLFIGGISYETTDESMNDYFSKYGKIEDCVVIKDNSTGRSKGFGFVTFETETEADACMEER
          SGSEEEQ.RKLF.GG....TTD..M..YF.KYG.I.DCVVI....T.RSKGFGFVTFETE.EADACM.ER
Retrocopy SGSEEEQSRKLFVGGLNHDTTDDGMREYFAKYGNITDCVVIREQGTDRSKGFGFVTFETEVEADACMDER

Parental  PHTLNNRQIDVKRAVSREESAKPGAHFQVKKIFIGGLKDGCDESSLKEYF---GKIGSIETFELPLERDS
          PH.L..R.IDVKRAVSREES.KPGAH.QVKKIF.GG.K.GCDE..L.EYF....K...I...E.PLERD.
Retrocopy PHVLDTRKIDVKRAVSREESSKPGAHTQVKKIFVGGVKEGCDEQTLREYFDSFSKRSLIQSVEIPLERDT

Parental  DKPRGFAFITFTDHDTVDKLVAKRHHYVNGVRCEVKKALSKSEMEKAKSQGKTIYFGCGGGGGRGGGSCV
          ..P.GFAF.TF.D.D.VDKLVA.RHH...G..C.VKKALSK.EME..K....T.....G..GG.G.G...
Retrocopy QRPKGFAFVTFEDFDIVDKLVARRHHDIAGFKCQVKKALSKQEMERSKQELETKQRWSGSRGGTGKGDYQ

Parental  FNGFFAGSGGYGGGGGYGDEGGYGSGGGGYGSGSGGGGYGGGSG-AGYGSGYGGYGSGESGYGGASGGGG
          ..G.....GGY.G.G.....G.Y....G.YG..S..G.YGGG.G..G..SGYG..G.G..GYGG...GGG
Retrocopy YGGY----GGYEGQG----HGNYRPMRGQYGQRS-SGPYGGGYGRGGSSSGYGSRGGGGGGYGGR--GGG

Parental  YSSGYGG
          YS...GG
Retrocopy YSKRGGG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ciona savignyi was not studied using RNA-Seq expression data.

ChIP-Seq

Ciona savignyi was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_csav_26 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_26 was not experimentally validated.

Homology

Retrocopy orthology:

Ciona savignyi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005726	4 retrocopies	retro_btau_1330, retro_btau_1535, retro_btau_193, retro_btau_228,
Choloepus hoffmanni	ENSCHOG00000013832	15 retrocopies	retro_chof_1060, retro_chof_1191, retro_chof_1413, retro_chof_1460, retro_chof_1507, retro_chof_2062, retro_chof_2135, retro_chof_2235, retro_chof_2263, retro_chof_2404, retro_chof_2425, retro_chof_2473, retro_chof_2574, retro_chof_499, retro_chof_853,
Ciona intestinalis	ENSCING00000004062	1 retrocopy	retro_cint_7,
Callithrix jacchus	ENSCJAG00000007908	2 retrocopies	retro_cjac_2285, retro_cjac_3041,
Ciona savignyi	ENSCSAVG00000000472	1 retrocopy	retro_csav_26 ,
Dasypus novemcinctus	ENSDNOG00000012928	1 retrocopy	retro_dnov_1978,
Dipodomys ordii	ENSDORG00000005482	1 retrocopy	retro_dord_489,
Echinops telfairi	ENSETEG00000018577	1 retrocopy	retro_etel_1368,
Felis catus	ENSFCAG00000027765	1 retrocopy	retro_fcat_692,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Myotis lucifugus	ENSMLUG00000007578	1 retrocopy	retro_mluc_34,
Mus musculus	ENSMUSG00000004980	1 retrocopy	retro_mmus_573,
Oryctolagus cuniculus	ENSOCUG00000026859	2 retrocopies	retro_ocun_1205, retro_ocun_642,
Otolemur garnettii	ENSOGAG00000015353	3 retrocopies	retro_ogar_1384, retro_ogar_3077, retro_ogar_3189,
Ochotona princeps	ENSOPRG00000011698	2 retrocopies	retro_opri_165, retro_opri_893,
Rattus norvegicus	ENSRNOG00000011175	3 retrocopies	retro_rnor_1824, retro_rnor_2043, retro_rnor_2339,
Ictidomys tridecemlineatus	ENSSTOG00000006202	3 retrocopies	retro_itri_1723, retro_itri_448, retro_itri_717,
Tursiops truncatus	ENSTTRG00000000709	3 retrocopies	retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,