RetrogeneDB ID: retro_xtro_24

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173091.1:32812..33943(-)
• Located in intron of: ENSXETG00000006581

Retrocopy information

• Ensembl ID: ENSXETG00000027434
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: acta1
• Ensembl ID: ENSXETG00000021417
• Aliases: None
• Description: actin, alpha 1, skeletal muscle [Source:Jamboree;Acc:XB-GENE-491938]

Sequence

>retro_xtro_24
ATGTGTGACGATGAGGAGACCACCGCTCTTGTCTGTGACAATGGCTCTGGGCTGGTGAAAGCTGGCTTTGCAGGAGATGA
TGCTCCCAGGGCAGTGTTCCCATCTATTGTGGGTCGCCCACGTCACCAGGGAGTCATGGTAGGCATGGGACAGAAGGACT
CCTATGTTGGGGATGAAGCCCAAAGCAAGAGGGGTATCCTCACCCTGAAGTATCCCATTGAGCATGGCATAATCACTAAC
TGGGACGACATGGAAAAGATCTGGCATCACACCTTCTACAATGAACTTCGTGTTGCCCCTGAAGAGCACCCTACACTGCT
AACAGAAGCTCCACTTAACCCAAAAGCCAACAGAGAAAAGATGACACAGATCATGTTTGAAACCTTCAATGTGCCAGCCA
TGTATGTTGCAATCCAAGCCGTGCTGTCTCTCTATGCCTCTGGTCGTACCACTGGTATTGTGCTGGACTCTGGAGATGGT
GTCACCCACAATGTCCCCATATATGAAGGTTATGCTCTGCCTCATGCCATCATGCGTCTGGACCTGGCAGGTCGCGACCT
GACTGACTACCTCATGAAGATCCTAACTGAACGTGGGTACTCATTTGTTACAACAGCAGAAAGGGAAATTGTGCGTGACA
TCAAGGAAAAGTTGTGCTATGTTGCCCTGGACTTTGAAAATGAAATGGCAACAGCTGCATCATCCTCTTCCCTGGAAAAG
AGTTATGAATTACCAGACGGTCAAGTTATCACCATTGGTAATGAGCGTTTCCGCTGCCCCGAGACCCTGTTCCAGCCTTC
TTTCATCGGCATGGAATCTGCTGGCATTCATGAGACCACCTACAACAGCATCATGAAATGTGACATTGACATCCGCAAGG
ACTTGTATGCCAACAATGTTCTCTCTGGTGGTACCACAATGTACCCAGGTATTGCCGACCGTATGCAGAAGGAAATCACT
GCTCTGGCTCCAAGCACCATGAAAATCAAGATCATTGCACCACCCGAACGCAAGTACTCTGTCTGGATTGGAGGTTCTAT
TCTTGCATCTCTCTCAACCTTCCAGCAAATGTGGATCACCAAGCAAGAATACGATGAAGCTGGACCTTCCATTGTCCACC
GTAAATGCTTC

Alignment

ORF - retro_xtro_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDDEETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK
          MCDDEETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK
Retrocopy MCDDEETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK

Parental  YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQA
          YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQA
Retrocopy YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQA

Parental  VLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREI
          VLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREI
Retrocopy VLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREI

Parental  VRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETT
          VRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETT
Retrocopy VRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETT

Parental  YNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS
          YNSIMKCDIDIRKDLYANNV.SGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS
Retrocopy YNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS

Parental  LSTFQQMWITKQEYDEAGPSIVHRKCF
          LSTFQQMWITKQEYDEAGPSIVHRKCF
Retrocopy LSTFQQMWITKQEYDEAGPSIVHRKCF

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	0.28 RPM	8.86 RPM
SRP007412_heart	337.63 RPM	17421.20 RPM
SRP007412_kidney	337.63 RPM	17421.20 RPM
SRP007412_liver	0.00 RPM	26.57 RPM
SRP007412_skeletal_muscle	787.53 RPM	63692.60 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_24 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_24 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000014347	1 retrocopy	retro_nleu_1585,
Ochotona princeps	ENSOPRG00000002854	1 retrocopy	retro_opri_573,
Xenopus tropicalis	ENSXETG00000021417	1 retrocopy	retro_xtro_24 ,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,