RetrogeneDB ID: retro_xtro_71

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL191971.1:1245..2052(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXETG00000033956
• Aliases: None
• Description: None

Sequence

>retro_xtro_71
CCGGCTTATGCGCGGGTTATTAATTCAGTAAGGATGGAGTTCGAGAAGGAGAAGAGAGGAGACAGAGGAATTGAATACAT
TGTTAAAGTTTTGCTGTTTGGGTTTTTTCAGTTCACTGCAGATAAGATTTTGGCTCTTCAGGATTATCATTTAAGAGGAG
TTTACGATATCACTTTTGTTAATAAGAAGACCTGTATTGACTTTGTAAAGAAAATGGAGCAACATCACAGCAATGATTTA
TTAAAAGGCATTAAAATAACACTGCATTATGAAGTTGAAGATGTGAGACCATTGGTGGTAAAAATGTATAATCCGAATGT
ACCCCAAGAAGATGTTACAAACTGGCTTTTAATGTACTGTGATAAAGTGAAATTCTTACACAATATTGTGAATCAATTCG
GGTTATGGACTGGAAAAAGAAAGTTTTTAGTTTCTTTTAAAAAGGGAATTTTACCACCTGCACGTTTTAGTATTGGGAAA
TATAATGGTGACTTATTTTATGATGGGATGGGCAGTTTTTGCAGACTTTGTCATGAATATGGCCATACAATTGAGGACTG
TAAACAAGTGTGTCGATGCAGAAATTGTGATTCCTTCAAACACACTACAAAGGAATGTTCCAAAGAAAAGAGATGCAATT
TTTGTTTCAATACTGGCCATGTGTATTTTAATTGCCCTAATCGAAGTCGTGAGAAAATGCGACATGCTGTTCCTGAAGGA
AAACCATCTGTTGAGAGGCATGCTACTCCTGTTTTAGTTCTGGCTGCTAAGCAAGCATCACAGAGTGCATCTGATCTGAC
TTCCACT

Alignment

ORF - retro_xtro_71 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.21 %
• Parental protein coverage: 98.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKFYLMKNSVRIIATGEDLSVEKWLSYVVDVILGDFGRVRRAEILAIQDYLRRGVFDVTFDVDGIFSSFL
          P......NSVR.....E.........Y.V.V.L..F.......ILA.QDY..RGV.D.TF........F.
Retrocopy PAYARVINSVRMEFEKEKRG-DRGIEYIVKVLLFGFFQFTADKILALQDYHLRGVYDITFVNKKTCIDFV

Parental  KIWQQSPDDVRLVGFKIIPHFNEEVT--LVIMSYSPFVPLGEIEAFLWRYCKKVSFVGHVLNKLGIWTSK
          K...Q......L.G.KI..H...E....LV...Y.P.VP.......L..YC.KV.F.....N..G.WT.K
Retrocopy KKMEQHHSNDLLKGIKITLHYEVEDVRPLVVKMYNPNVPQEDVTNWLLMYCDKVKFLHNIVNQFGLWTGK

Parental  YRFKVVLRKKGILPPARFSIGKYNGDLFYDGMGSFCRLCHEYGHTIEDCKQVCRCRNCDSFKHTTKECSK
          ..F.V...KKGILPPARFSIGKYNGDLFYDGMGSFCRLCHEYGHTIEDCKQVCRCRNCDSFKHTTKECSK
Retrocopy RKFLVSF-KKGILPPARFSIGKYNGDLFYDGMGSFCRLCHEYGHTIEDCKQVCRCRNCDSFKHTTKECSK

Parental  EKRCNFCFNTGHVYFNCPNRSREKMRHAVPEGKPSVERHATPVLVLAAKQASQSASDLTST
          EKRCNFCFNTGHVYFNCPNRSREKMRHAVPEGKPSVERHATPVLVLAAKQASQSASDLTST
Retrocopy EKRCNFCFNTGHVYFNCPNRSREKMRHAVPEGKPSVERHATPVLVLAAKQASQSASDLTST

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	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_71 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_71 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000024706	1 retrocopy	retro_xtro_32,
Xenopus tropicalis	ENSXETG00000026344	1 retrocopy	retro_xtro_4,
Xenopus tropicalis	ENSXETG00000033956	2 retrocopies	retro_xtro_22, retro_xtro_71 ,