RetrogeneDB ID: retro_ptro_2827

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:38394075..38394783(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX2
• Ensembl ID: ENSPTRG00000033702
• Aliases: None
• Description: None

Sequence

>retro_ptro_2827
AGAGAAGCGGAGATCCTGATGTTTCTCAGTGCCATTGTGATGATGAAGAACCGCAGATCCATCACTGTGGAGCAACACAT
AGGCAACATTTTCATGTTTAGTAAAGTGGCCAACGCAATTCTTTTCTTCCGCTTGGATATTCGCATGGGCCTACTTTACA
TCACACTCTGCATAGTGTTCCTGATGACGTGCAAACCCCCGCCCCCCCCCCCATATATGGGCCCTGAGTATATCAAGTAC
TTCAATGATAAAACCATTGATGAGGAACTAGAACGGGACAACAGGGTCACTTGGATTGTGGAGTTCTTTGCCAATTGATC
TAATGACTGCCAATCATTTGCCCCTATCTATGCTGACCTCTCCCTTAAGTACAACTGTACAGGGCTAAATTTTGGGACGG
TGGATGCTGGACGCTATACTGATGTTAGTACGCGGTACAAAGTGAGCACATCACCCCTCACCAATCAACTCCCTACCCTG
ATCCTGTTCCAAGGTGGCAAGAAGGTAATGCGGCAGCCACAGACTGACAAGAAAGGACGGGCTGTCTCATGGACCTTCTC
TGAGGAGAATGTGATCCGAGAATTTAACTTAAATGAGCTATACCAGCGGGCCAAGAAGCTATCAAAGGCTGGAGACGATA
TCCCTGAGGAGCAGCCTGTGGCTTCAACCCCCACCACAGTGTCAGATGGGGAAAGCAAGAAGGATAAA

Alignment

ORF - retro_ptro_2827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.95 %
• Parental protein coverage: 78.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REVEILMFLSAIVMMKNRRSITVEQHIGNIFMFSKVANTILFFRLDIRMGLLYITLCIVFLMTCKPPL--
          RE.EILMFLSAIVMMKNRRSITVEQHIGNIFMFSKVAN.ILFFRLDIRMGLLYITLCIVFLMTCK.....
Retrocopy REAEILMFLSAIVMMKNRRSITVEQHIGNIFMFSKVANAILFFRLDIRMGLLYITLCIVFLMTCKXXXXX

Parental  -YMGPEYIKYFNDKTIDEELERDKRVTWIVEFFANWSNDCQSFAPIYADLSLKYNCTGLNFGKVDVGRYT
          .YMGPEYIKYFNDKTIDEELERD.RVTWIVEFFAN.SNDCQSFAPIYADLSLKYNCTGLNFG.VD.GRYT
Retrocopy XYMGPEYIKYFNDKTIDEELERDNRVTWIVEFFAN*SNDCQSFAPIYADLSLKYNCTGLNFGTVDAGRYT

Parental  HVSTRYKVSTSPLTKQLPTLILFQGGKEVMRRPQIDKKGRAVSWTFSEENVIREFNLNELYQRAKKLSKA
          .VSTRYKVSTSPLT.QLPTLILFQGGK.VMR.PQ.DKKGRAVSWTFSEENVIREFNLNELYQRAKKLSKA
Retrocopy DVSTRYKVSTSPLTNQLPTLILFQGGKKVMRQPQTDKKGRAVSWTFSEENVIREFNLNELYQRAKKLSKA

Parental  GDNIPEEQPVASTPTTVSDGENKKDK
          GD.IPEEQPVASTPTTVSDGE.KKDK
Retrocopy GDDIPEEQPVASTPTTVSDGESKKDK

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_prefrontal_cortex	4.56 RPM	80.51 RPM
SRP007412_cerebellum	5.92 RPM	67.86 RPM
SRP007412_heart	2.68 RPM	39.55 RPM
SRP007412_kidney	4.05 RPM	60.23 RPM
SRP007412_liver	1.87 RPM	29.23 RPM
SRP007412_testis	1.69 RPM	32.98 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2827 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2827 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4158

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035426	1 retrocopy	retro_cjac_3263,
Homo sapiens	ENSG00000213593	1 retrocopy	retro_hsap_4158,
Monodelphis domestica	ENSMODG00000020112	1 retrocopy	retro_mdom_924,
Mus musculus	ENSMUSG00000050043	1 retrocopy	retro_mmus_154,
Pan troglodytes	ENSPTRG00000033702	1 retrocopy	retro_ptro_2827 ,