RetrogeneDB ID: retro_xtro_58

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL181586.1:5444..6299(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: etfdh
• Ensembl ID: ENSXETG00000019489
• Aliases: None
• Description: electron-transferring-flavoprotein dehydrogenase [Source:Jamboree;Acc:XB-GENE-972267]

Sequence

>retro_xtro_58
CGTGAGTCCATGGAATACGGCGTGGTGGTCGTGGGCGGCGGCCCGGCGGGCCTGGCCGCCGCCATCCGCATCAAGCAACT
GGCGACCGAGCACGGCTCGGATGTCTCCGTCGTCGTGCTGGAAAAAGGCTCCGAGCCCGGTGCGCACATTCTCTCGGGCG
CCATCATGGATCCGCGCGCGCTCACCGAGCTGATCCCCGACTGGAAGGAAAAAGGCGCACCCCTGAACCAGCCCGTCACC
GACGATGCCTATGTCTTCCTGTCCGAGCAATCGGCCTTCCGCGTCCCCAACATCGTCCTGCCGCCCTTCGCGCACAACCA
CGGCAACTACGTCGTGCGCCTGGGTGACGTGACCAAATGGCTGGCCGAACAGGCCGAAAGCCTGGGCGTGGAAATCTTCC
CCGGCTTCCCCGCCACCGAAGTGCTCTACAACGACGACGGCTCCGTCAAAGGGGTTGCCACCGGCAATATGGGCATCGGC
AAAGACGGCGAACCTACCGAGAACTTCCAACTCGGCATGGAACTGCTGGCCAAGTACACCATCTTTGCCGAAGGCGCGCG
CGGCCACCTGGGCAAGCAGCTCATCGCCCGCTACCGGCTCGACGACAACCGCGACCCGCAAAGCTTCGGTATCGGCGTCA
AGGAACTGTGGGAGATCGATCCCAAGAAACACCAGCCCGGCTTCGTCATGCATACCGCTGGCTGGCCCATGGACAGCAAA
ACCTATGGCGGCGCTTTCCTGTACCACCTGGAGGGCCACAAGGTGGTGCTGGGCTTTGTCACGGGGTTGGGCTATGCCAA
TCCGTATCTGAGTCCGTTCGAGGAGTTCCAGCGCTGGAAGACGCATCCCAACATC

Alignment

ORF - retro_xtro_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.01 %
• Parental protein coverage: 50.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFAEEADVVIVGGGPAGLSAAIRLKQLAAECDKELRVCLVEKGAQIGAHTLSGACLEPRALEELFPDWKE
          R...E..VV............IR.KQLA.E......V...EKG...GAH.LSGA...PRAL.EL.PDWKE
Retrocopy RESMEYGVVVXXXXXXXXXXXIRIKQLATEHGSDVSVVVLEKGSEPGAHILSGAIMDPRALTELIPDWKE

Parental  RGAPLNTPVTEDKFGILTKKHRIPVPILPGLPM-NNHGNYIVRLGHFVSWLGEQAEALGVEIYPGYAASE
          .GAPLN.PVT.D....L.......VP.....P...NHGNY.VRLG....WL.EQAE.LGVEI.PG..A.E
Retrocopy KGAPLNQPVTDDAYVFLSEQSAFRVPNIVLPPFAHNHGNYVVRLGDVTKWLAEQAESLGVEIFPGFPATE

Parental  VLFHEDGSVKGIATNDVGIHKDGSPKSTFERGLELHAKVTIFGEGCHGHLAKQLYNKFNLRQNCEPQTYA
          VL...DGSVKG.AT...GI.KDG.P...F..G.EL.AK.TIF.EG..GHL.KQL.....L..N..PQ...
Retrocopy VLYNDDGSVKGVATGNMGIGKDGEPTENFQLGMELLAKYTIFAEGARGHLGKQLIARYRLDDNRDPQSFG

Parental  IGLKELWVIDEKKWKPGCVEHTVGWPLDRHTYGGSFLYHLNEGEPLVALGLVVGLDYQNPFINPFRELQR
          IG.KELW.ID.KK..PG.V.HT.GWP.D..TYGG.FLYHL.EG...V.LG.V.GL.Y.NP...PF.E.QR
Retrocopy IGVKELWEIDPKKHQPGFVMHTAGWPMDSKTYGGAFLYHL-EGHKVV-LGFVTGLGYANPYLSPFEEFQR

Parental  WKHHPSV
          WK.HP..
Retrocopy WKTHPNI

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	19.73 RPM
SRP007412_heart	0.00 RPM	83.24 RPM
SRP007412_kidney	0.00 RPM	83.24 RPM
SRP007412_liver	0.00 RPM	104.50 RPM
SRP007412_skeletal_muscle	0.00 RPM	73.48 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_58 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_58 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000004905	1 retrocopy	retro_itri_481,
Xenopus tropicalis	ENSXETG00000019489	1 retrocopy	retro_xtro_58 ,