RetrogeneDB ID: retro_xtro_42

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL175336.1:2626..3832(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: gcdh
• Ensembl ID: ENSXETG00000007932
• Aliases: None
• Description: glutaryl-CoA dehydrogenase [Source:Jamboree;Acc:XB-GENE-1016447]

Sequence

>retro_xtro_42
CACTGACTGGAGACACCGATGGCCCATGCCCCCTTCCACTGGGAAGACCCGTTCCTGCTCGACCAACAGCTCAGCGCCGA
CGAGCGCGCCATCCGCGACGCCGCCGCCGCTTACTGCCAGGGCCAGTTGGCCCCGCGCGTGCGGGACATGTTCCGCCACG
AGAAGACCGATACCGCCATCTTCCGTGAGATGGGCGCGCTCGGCCTGCTCGGGCCCACGATTCCCGAGGCCTACGGCGGC
GCGGGTCTGAATTACGTCAGCTACGGCCTGATCGCGCGCGAGATCGAGCGCGTGGATTCGGGCTACCGCTCCATGGCGTC
CGTGCAGTCGTCGCTGGTGATGGTGCCGATCCACACCTTCGGCACCGAGGCGCAGAAGCAGAAGTACCTGCCCGGACTGG
CTTCGGGCGCGCTCATCGGCTGCTTCGGCCTGACGGAGCCGGATCATGGCTCCGATCCGGGCAGCATGGCCGCGCGCGCC
ACCAAGGTGGCTGGCGGCTACCGGCTCAAGGGCAGCAAGATGTGGATCACCAATTCACCGGTGGCGGATGTGTTCGTGGT
CTGGGCCAAGGAAGTGAGCGAGGGCGGCGCCGTGGGCCCGATCCGCGGCTTCGTGCTGGAGAAGGGCTGGAAGGGGCTTG
CCGCCCCGGCCATCCATGGCAAGGTGGGGCTGCGCACCAGTATCACGGGCGAGATCGTCATGGACGATGTGTTCGTGCCC
GAGGAAAACGCCTTTCCCGAGGTGCACGGCCTCAAGGGCCCGTTCACCTGCCTGAACAGCGCGCGCTATGGCATTGCCTG
GGGCGCCATGGGTGCGGCCGAGTTCTGCTGGCACACCGCCCGCCAGTACACGCTGGAGCGCCAGCAGTTCGGTCGCCCGC
TGGCGGCCAACCAGCTCGTGCAGAAAAAGCTGGCCGATATGCAGACCGAGATCGCCCTGGGCCTGCAGGCCGCGCTGCGC
TTCGGCCGCATGAAGGATGAAGGTATCGCCGCCGTGGAGGGCACTTCGCTCATCAAGCGCAACAACTGCGGCAAGGCCCT
GGACATCGCCCGTCTGGCGCGCGACATGCTCGGCGGCAACGGCATCAGCGACGAGTTCGGCGTGGCGCGCCATCTGGTGA
ATCTGGAGGTGGTCAATACCTACGAGGGCACGCATGACGTGCACGCGCTCATCCTGGGGCGGGCGCAGACGGGTATCGCA
GCATTC

Alignment

ORF - retro_xtro_42 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.88 %
• Parental protein coverage: 90.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HEKKSSKSRVQFDYQDALSLDSQLTEDEIMIRDSFRAYCQEKLMPRILMANRKEVFERDIISEMGELGVL
          H..........F...D...LD.QL..DE..IRD...AYCQ..L.PR.....R.E.....I..EMG.LG.L
Retrocopy H*LETPMAHAPFHWEDPFLLDQQLSADERAIRDAAAAYCQGQLAPRVRDMFRHEKTDTAIFREMGALGLL

Parental  GSTI-KGYGCAGTSYVAYGLLAREVERVDSSYRSVMSVQSSLVMHPIAAYGSEEQKQKYLPRLASGEWLG
          G.TI...YG.AG..YV.YGL.ARE.ERVDS.YRS..SVQSSLVM.PI...G.E.QKQKYLP.LASG...G
Retrocopy GPTIPEAYGGAGLNYVSYGLIAREIERVDSGYRSMASVQSSLVMVPIHTFGTEAQKQKYLPGLASGALIG

Parental  CFGLTEPNHGSDPAGMETRARYNPSSKTYTLNGAKTWITNSPIADLCVVWA--ICEDGKV---RGFLIER
          CFGLTEP.HGSDP..M...AR.......Y.L.G.K.WITNSP.AD..VVWA....E.G.V...RGF..E.
Retrocopy CFGLTEPDHGSDPGSMA--ARATKVAGGYRLKGSKMWITNSPVADVFVVWAKEVSEGGAVGPIRGFVLEK

Parental  GTKGLSTPKIEGKFSLRASATGMILLEDVEIPEENLLPNVSGLGGPFGCLNNARYGISWGALGAAEFCFH
          G.KGL..P.I.GK..LR.S.TG.I...DV..PEEN..P.V.GL.GPF.CLN.ARYGI.WGA.GAAEFC.H
Retrocopy GWKGLAAPAIHGKVGLRTSITGEIVMDDVFVPEENAFPEVHGLKGPFTCLNSARYGIAWGAMGAAEFCWH

Parental  TARQYTLDRIQFGVPLARNQLIQKKLADMLTDITIGLQACLRLGRLKDEEKATPEMISMLKRNSCGKALD
          TARQYTL.R.QFG.PLA.NQL.QKKLADM.T.I..GLQA.LR.GR.KDE..A..E..S..KRN.CGKALD
Retrocopy TARQYTLERQQFGRPLAANQLVQKKLADMQTEIALGLQAALRFGRMKDEGIAAVEGTSLIKRNNCGKALD

Parental  IARQARDMLGGNGISDEYHIIRHVMNLESVNTYEGTHDVHALILGRAITGLQAF
          IAR.ARDMLGGNGISDE....RH..NLE.VNTYEGTHDVHALILGRA.TG..AF
Retrocopy IARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDVHALILGRAQTGIAAF

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	0.00 RPM	43.27 RPM
SRP007412_heart	0.00 RPM	49.81 RPM
SRP007412_kidney	0.00 RPM	49.81 RPM
SRP007412_liver	0.02 RPM	142.45 RPM
SRP007412_skeletal_muscle	0.00 RPM	65.96 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_42 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_42 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000001085	1 retrocopy	retro_xtro_10,
Xenopus tropicalis	ENSXETG00000007932	1 retrocopy	retro_xtro_42 ,
Xenopus tropicalis	ENSXETG00000016078	1 retrocopy	retro_xtro_43,