RetrogeneDB ID: retro_xtro_31

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173396.1:189530..190811(-)
• Located in intron of: ENSXETG00000034208

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: XB-GENE-5822524
• Ensembl ID: ENSXETG00000024377
• Aliases: None
• Description: zinc finger protein [Source:Jamboree;Acc:XB-GENE-5822524]

Sequence

>retro_xtro_31
CACAACCACCAGCAAATTCACACAGGAGAGAAACCTTTCTCGTGCCCAGAATGTGGGAAATGTTTCTCTCAAAAGACCCA
TCTCCAACGGCATCAGAAAACTCACACAGGGGAGAAACCATTCACATGCGCAGAATGCGGGAAGAACTTCACTCAGAAGA
TCACCCTTGTCAAACACCAGGCTATTCACACTGGGGAGAAACCATTCATGTGCATAGAATGCGGGAAATACTTCTCTCAG
AAGAGCCATCTTTGCAGTCACCAAAAAATTCACACAGGGGAGAAATGTTTTTTGTGTATAGTTTGTGGGAAAAGCTTCTC
TCATAAGTGCAGCCTTATGAACCATCAGATGATCCACACAGGGGAGAAACCATACACCTGCACAGAATGCGGGAAGAGCT
TCTCTCGCAAGCATTATCTTCAGATCCACAAACAAACTCACACAGGGGATAAACCTTACAAATGTACAGACTGTGGGAAA
AGTTTCTCTCAGAAGAGCCACATTTACAGTCACCGGAAAATCCACTCAGGGGTGAAACCTTACACGTGCACTACATGTGG
GAAGAGCTTTTTTCACAAGATTAGCCTTATGAGCCACCAGATGATTCATACCGGAGAGAAACCATTCGCCTGTATCGAAT
GTGGCAAAAGCTTCTCTGAAAAGAGCAAACTCCTGAAACACTGGAGAGTTCACACAGGAGAGAAACCTTTCACGTGCACG
ATCTGTGGGAAAAGCTTTTCTCTCAAGGTTCATCTTCAGACTCATCAAGTGACTCACACAGGAGAAAAGCCATTCGCGTG
CTCCGAATGTGGGAAAAGGTTTGCACGAAAGAGCAACCTTCAAGGGCATCAGAAAACTCACACAGGGGATAAACCTTTCT
CGTGCACAGAATGCGGGCGAAGATTCACGGAAAAGAACAAACTTCTCAGGCACTGGCAGATTCACTCGGGGGAGAGATCT
TTCCTATGCGCCACGTGCGGGAAAGGCTTTTCCATCAGAGCTGATCTTCGCAACCATCAGATGGTTCACACCGGGGAGAA
ACCATTCACTTGCACAGAATGCGGCAAGAGCTTCTCCCGAAAGAGCATCCTTCAGGGCCATCGGAAAACTCACACAGGGG
AGAAACCATTTGCATGTACAGAATGTGGCAAATGCTTCTCTGCCAGCGGGATACTTGTCAGGCACCAGAGGGTTCACACG
GGAGAGAAACCTTTTATCTGTGCAGAATGTGGCGGGTGCTTCTCCCAAAAGAGTATCCTTCTGCGACACCAAAAGACTCA
C

Alignment

ORF - retro_xtro_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.95 %
• Parental protein coverage: 50.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HHHNKIHTGEKPFICTECGKGFTQKTSLLNHNKIHTGEKPFTCTECGRSFTEKKTLRNHSKIHTGEKPFT
          H.H..IHTGEKPF.C.ECGK.F.QKT.L..H.K.HTGEKPFTC.ECG..FT.K.TL..H..IHTGEKPF.
Retrocopy HNHQQIHTGEKPFSCPECGKCFSQKTHLQRHQKTHTGEKPFTCAECGKNFTQKITLVKHQAIHTGEKPFM

Parental  CSDCGKSFAQIISLQNHVTIHTGEKPFTCTECGKSFSERKTLRDHSKIHTGEKPFTCTDCGKSFIQRKTL
          C..CGK.F.Q...L..H..IHTGEK.F.C..CGKSFS....L..H..IHTGEKP.TCT.CGKSF.....L
Retrocopy CIECGKYFSQKSHLCSHQKIHTGEKCFLCIVCGKSFSHKCSLMNHQMIHTGEKPYTCTECGKSFSRKHYL

Parental  RNHTKIHTGERPYACTECGKSFTEKKTLRDHTKIHTGEKPFTCTECGKSFTEKSHLRSHNKIHTGEKPFT
          ..H...HTG..PY.CT.CGKSF..K.....H.KIH.G.KP.TCT.CGKSF..K..L.SH..IHTGEKPF.
Retrocopy QIHKQTHTGDKPYKCTDCGKSFSQKSHIYSHRKIHSGVKPYTCTTCGKSFFHKISLMSHQMIHTGEKPFA

Parental  CTECGKSFTEKRNLQHHYNVHTGEKPYTCADCGKAFSQKINLQNHQNIHTGEKPFTCSECGKSLACKGSL
          C.ECGKSF.EK..L..H..VHTGEKP.TC..CGK.FS.K..LQ.HQ..HTGEKPF.CSECGK..A.K..L
Retrocopy CIECGKSFSEKSKLLKHWRVHTGEKPFTCTICGKSFSLKVHLQTHQVTHTGEKPFACSECGKRFARKSNL

Parental  ERHQMSHIGVKPFTCTECGKSFTEKNSLRKHERIHTGEKPFSCIECGRSFNLKHNLEKHKKSHTGEKPFT
          ..HQ..H.G.KPF.CTECG..FTEKN.L..H..IH.GE..F.C..CG..F.....L..H...HTGEKPFT
Retrocopy QGHQKTHTGDKPFSCTECGRRFTEKNKLLRHWQIHSGERSFLCATCGKGFSIRADLRNHQMVHTGEKPFT

Parental  CTECGRSFTKKSTLHIHQTSHTGEKPFTCTECGRGFTDKNNLKNHKRIHTGEKPFTCTECGKCFTERGAV
          CTECG.SF..KS.L..H...HTGEKPF.CTECG..F.....L..H.R.HTGEKPF.C.ECG.CF......
Retrocopy CTECGKSFSRKSILQGHRKTHTGEKPFACTECGKCFSASGILVRHQRVHTGEKPFICAECGGCFSQKSIL

Parental  RVHKKVH
          ..H.K.H
Retrocopy LRHQKTH

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	5.95 RPM	9.55 RPM
SRP007412_heart	3.10 RPM	3.48 RPM
SRP007412_kidney	3.10 RPM	3.48 RPM
SRP007412_liver	0.63 RPM	3.82 RPM
SRP007412_skeletal_muscle	2.03 RPM	1.17 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_31 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_31 was not experimentally validated.

Homology

Retrocopy orthology:

Xenopus tropicalis 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000022348	1 retrocopy	retro_acar_50,
Anolis carolinensis	ENSACAG00000024100	1 retrocopy	retro_acar_28,
Anolis carolinensis	ENSACAG00000024147	1 retrocopy	retro_acar_46,
Danio rerio	ENSDARG00000089344	1 retrocopy	retro_drer_10,
Xenopus tropicalis	ENSXETG00000024377	1 retrocopy	retro_xtro_31 ,