RetrogeneDB ID: retro_csav_27

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_51:514272..515175(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000002434
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSA.10368
• Ensembl ID: ENSCSAVG00000004266
• Aliases: None
• Description: Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:H2YP82]

Sequence

>retro_csav_27
GATTTGGACAAAATGCTTGAAATTGCTAAACAGTGTAAATATCTTCCGGAATATGATTTAAAGAAATTGTGCGATTATGT
ATGTGATCTACTGCTAGAGGAGTCAAATGTCCAACCTGTATCAACACCAGTTACAGTTTGCGGAGACATCCATGGTCAAT
TTTACGACCTACAAGAGCTTTTCAAGACTGGAGGGGAAGTGCCTGACACAAACTACATTTTCATGGGCGATTTTGTGGAT
AGAGGATATTACAGTTTGGAAACATTGACATGTCTGCTAACATTAAAGGCTAAATGGCCAAACAAGATCACATTATTGAG
AGGAAATCACGAAAGTCGTCAAATCACACAGGTGTATGGGTTTTATGATGAGTGCCAGACAAAGTATGGAAATGCCAATG
CATGGAGATACTGTACTAAGGTGTTCGACTTGCTAACAATTGCGGCAATAATAGATTCCACGATACTCTGTGTTCATGGT
GGCCTTTCGCCGGATGTAAAAACCCTGGATCAAATTCGCACCATAGACCGCCAGCAAGAGATCCCACATAAAGGAGCGTT
TTGCGACCTCGTGTGGTCGGATCCAGAGGATGTAGACACATGGGCGATATCCCCTCGAGGGGCTGGTTGGTTATTTGGAG
CTAAAGTAACCAACGAGTTTGTCCATCTCAACAATCTTTCTCTTATCTGTCGGGCACATCAACTCGTACACGAAGGCTTC
AAGTACATGTTTGGTGAGAAACTGGTTACTGTATGGTCGGCTCCTAACTATTGCTACAGATGTGGAAATATTGCTGCAAT
TCTTGTGGTGCATACCAAAGAAGACAGAGAAGCAAAACTTTTTCGTGCAGTTCCTGATAATTTGAGAGTTATTCCAGAGC
GCAATACAACGCCGTACTTCCTT

Alignment

ORF - retro_csav_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.26 %
• Parental protein coverage: 96.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLDRQIEQLKRCEIIKESEVKALCAKAREILVEESNVQRVDSPVIVCGDIHGQFYDLTELFKVGGDMPDT
          DLD...E..K.C....E...K.LC......L.EESNVQ.V..PV.VCGDIHGQFYDL.ELFK.GG..PDT
Retrocopy DLDKMLEIAKQCKYLPEYDLKKLCDYVCDLLLEESNVQPVSTPVTVCGDIHGQFYDLQELFKTGGEVPDT

Parental  NYLFLGDFVDRGFYSVETFLLLLALKVRYPDRIVLIRGNHESRQITQVYGFYDECLRKYGSITVWRYCTE
          NY.F.GDFVDRG.YS.ET...LL.LK...P..I.L.RGNHESRQITQVYGFYDEC..KYG....WRYCT.
Retrocopy NYIFMGDFVDRGYYSLETLTCLLTLKAKWPNKITLLRGNHESRQITQVYGFYDECQTKYGNANAWRYCTK

Parental  IFDYLSLSAIIDGRIFCVHGGLSPSIQTLDQIRTIDRKQEVPHDGPMCDLLWSDPEDTTGWGVSPRGAGY
          .FD.L...AIID..I.CVHGGLSP...TLDQIRTIDR.QE.PH.G..CDL.WSDPED...W..SPRGAG.
Retrocopy VFDLLTIAAIIDSTILCVHGGLSPDVKTLDQIRTIDRQQEIPHKGAFCDLVWSDPEDVDTWAISPRGAGW

Parental  LFGSDVVSNFNHQNDIDMICRAHQLVMEGFKWHFNETVLTVWSAPNYCYRCGNVAAIFALDEHLKREFII
          LFG..V...F.H.N....ICRAHQLV.EGFK..F.E...TVWSAPNYCYRCGN.AAI........RE...
Retrocopy LFGAKVTNEFVHLNNLSLICRAHQLVHEGFKYMFGEKLVTVWSAPNYCYRCGNIAAILVVHTKEDREAKL

Parental  FEAAPQETRGLPVKKPLPDYFL
          F.A.P...R..P.....P.YFL
Retrocopy FRAVPDNLRVIPERNTTP-YFL

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_27 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_27 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.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015223	1 retrocopy	retro_amel_286,
Canis familiaris	ENSCAFG00000017089	1 retrocopy	retro_cfam_16,
Ciona savignyi	ENSCSAVG00000004266	1 retrocopy	retro_csav_27 ,
Equus caballus	ENSECAG00000022179	1 retrocopy	retro_ecab_911,
Felis catus	ENSFCAG00000014171	1 retrocopy	retro_fcat_1043,
Macropus eugenii	ENSMEUG00000000397	5 retrocopies	retro_meug_1014, retro_meug_1188, retro_meug_1336, retro_meug_560, retro_meug_859,
Ornithorhynchus anatinus	ENSOANG00000008136	1 retrocopy	retro_oana_25,
Pan troglodytes	ENSPTRG00000007984	1 retrocopy	retro_ptro_28,
Tursiops truncatus	ENSTTRG00000005532	1 retrocopy	retro_ttru_1015,