RetrogeneDB ID: retro_xtro_28

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173205.1:401933..403111(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXETG00000030588
• Aliases: None
• Description: None

Sequence

>retro_xtro_28
AACCTATATACTATGCAACTACATATTGCCTCACTTAACTTCAAAGGACTTTAATAGTCCACAAAAAAGGAAACTACTAC
TAAATTGGGCTCAAGACTCCAAAATAGATATATTATATATACAGGAAACTCATCTGACTGGTAAGGATCACCCAAAACTG
CTTTCAAAAAACTTTAACAAGACCATTTACACTAACGCTCCCATTAAAAAAAATGGTGTGGCTATCCTATTCAGGAAGTC
CCTTCCTATTAAAATCACTAAGGTCCAAGCAGACAAAAAAGGTAGATTCCTAATTGTTAACTTAGAAGTGTTATCCCAAT
CATTTTTACTAATGAATATTTACGCTCCAAATTTCCATCAAATGGCTTTTATAAACAAACTATTTTGTAAAGTGAAACAA
GAAACCAATGTTAAACTCCTAATTACCAGGGACTTTAACCTGTCTCCCGACCCACTCATAGACAAAGCCCCCACTCCAAA
AGGAAACACCCTAAGAACTGCCACTTGTCTTTCAAAGGCCTTTTTTAAAACTATAAAGCAAATGGAACTATATGATGTAT
TGAGAGCAGGTCACCCTTCTGAGCGTGATTATACTTTTTTTTCACATGTACATTCCTCCTAATTCAAGGATTGATTTAAT
TCTTGCTGATAAGATCTCCTTATTGCAAATGGTCAAATCATATATAGAGATAGCCACCTGGTCGGACCATGCCCCAGTTG
CATGTTTCATAGATTTCCACCAAATTCTCAGCCCGTCCTTTAATTGGAGATTAAACAATACCTTATTACAGAATGAAAAA
CATGCTGAAAAAATAACAAAACTTACCGAGGAATATTTTAACCTGAATCTCTCCCCAGACACCTCTAATGATCTACTTTG
GTGTTCATATAAGGCCTTTATCAGAGGCTATCTAATAGCCATGGCTGCTAAGGAAAAGAAAAAAAGAAACACTAAAGCAG
CAGAGTTACTTGCTATACTAGCCAAAGTTACAAGACAACACAAGCTTCATCCAACTGACGAGCTGGCCCAAAAGGTGGCA
TCCCATAATAAAGAAATAAATGTTTTATGCATGGAAAAAGTTGCATACCAAATACTGCTGACAAAACAACGATACTACAT
AGAAGACAATACTTCTATAGACAAATACTACAGTAAACTATACAACTTAAAAGATGAC

Alignment

ORF - retro_xtro_28 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.17 %
• Parental protein coverage: 97. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NLYNMQLHIASLNVKGL-NSPQKRKLLLNWAQDSKIDIVCIQEAHLTGKDHPKLISKNFKETIYPNAPIK
          NLY.MQLHIASLN.KGL.NSPQKRKLLLNWAQDSKIDI..IQE.HLTGKDHPKL.SKNF..TIY.NAPI.
Retrocopy NLYTMQLHIASLNFKGL>NSPQKRKLLLNWAQDSKIDILYIQETHLTGKDHPKLLSKNFNKTIYTNAPIX

Parental  KNGVAILFRNSLPIKIIKVQADKKG-YLIVNLEVLSQPFLLMNLYAPNSHQMTFINIMCNGLLQGESI--
          ..GVAILFR.SLPIKI.KVQADKKG..LIVNLEVLSQ.FLLMN.YAPN.HQM.FIN.......Q......
Retrocopy XXGVAILFRKSLPIKITKVQADKKGRFLIVNLEVLSQSFLLMNIYAPNFHQMAFINKLFCKVKQETNVKL

Parental  -VEMDFNLSPDPLLDKAPTPKGNTLRTATRLSKAFFKTIKQMELYDVWRAGHHSERDYTFFSHVHSS-YS
          ....DFNLSPDPL.DKAPTPKGNTLRTAT.LSKAFFKTIKQMELYDV.RAGH.SERDY....HVHSS..S
Retrocopy LITRDFNLSPDPLIDKAPTPKGNTLRTATCLSKAFFKTIKQMELYDVLRAGHPSERDYXXXXHVHSS>NS

Parental  RIDLILTDKISLLQMVKSYIGVATWSDHAPVGCFIDFHQIPSPSFSWKLNNTLLQNKIHAEKITKLTEEY
          RIDLIL.DKISLLQMVKSYI..ATWSDHAPV.CFIDFHQI.SPSF.W.LNNTLLQN..HAEKITKLTEEY
Retrocopy RIDLILADKISLLQMVKSYIEIATWSDHAPVACFIDFHQILSPSFNWRLNNTLLQNEKHAEKITKLTEEY

Parental  FNLNSSPDTPNDLLWCSYKAFIRGHLIAIASKEKKIRNTKLTELIAELAEVTSQHKIHPTGELAQKVTSL
          FNLN.SPDT.NDLLWCSYKAFIRG.LIA.A.KEKK.RNTK..EL.A.LA.VT.QHK.HPT.ELAQKV.S.
Retrocopy FNLNLSPDTSNDLLWCSYKAFIRGYLIAMAAKEKKKRNTKAAELLAILAKVTRQHKLHPTDELAQKVASH

Parental  NKEINVLNMEKVAYQILLTKQRYYIEDNKNGRLLASKLKDARAD
          NKEINVL.MEKVAYQILLTKQRYYIEDN.......SKL.....D
Retrocopy NKEINVLCMEKVAYQILLTKQRYYIEDNTSIDKYYSKLYNLKDD

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	0.14 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_28 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_28 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000030588	2 retrocopies	retro_xtro_23, retro_xtro_28 ,