RetrogeneDB ID: retro_ggor_2792

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:38699319..38700257(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX2
• Ensembl ID: ENSGGOG00000001519
• Aliases: None
• Description: None

Sequence

>retro_ggor_2792
AGAGAAGTGGAGATCCTGATGTTTCTCAGTGCCATTGTGATGATGAAGAACCGCAGATCCATCACTGTGGAGCAACATAT
AGGCAACATTTTCATGTTTAGTAAAGTGGCCAACGCAATTCTTTTTTTCCGCTTGGATATTCGCATGGGCCTACTTTACA
TCACACTCTGCATAGTGTTCCTGATGACGTGCAAACCCCCCCCCCCCCCGCCCATGTATGGGCCCTGAGTATATCAAGTA
CTTCAATGATAAAACCACTGATGAGGAACTAGAACGGGACAACAGGGTCACTTGGATTGTGGAGTTCTTTGCCAATTGGT
CTAATGACTGCCAATCATTTGCCCCTATCTATGCTGACCTCTCCCTTAAGTACAACTGTACAGGGCTAAATTTTGGGACG
GTGGATGCTGGACGCTATACTGATGTTAGTACGCGGTACAAAGTGAGCACATCACCCCTCACCAATCAACTCCCTACCCT
GATCCTGTTCCAAGGTGGCAAGAAGGTAATGCGGCAGCCACAGACTGACAAGAAAGGACGGGCTGTCTCATGGACCTTCT
CTGAGGAGAATGTGATCTGAGAATTTAACTTAAATGAGCTATACCAGCGGGCCAAGAAGCTATCAAAGGCTGGAGACAAT
ATCCCTGAGGAGCAGCCTGTGGCTTCAACCCCCACCACAGTGTCAGACGGGGAAAGCAAGAAGGATAAATAAGATCCTCA
CTTTGGCAGTGCTTCCTCTCCTGTCAATTCCAGGCTCTTTCCATAACCACAAGCCTGAGGCTACAGCCTTTTATTTATGT
TTTCCCTTTGGCTGTGACTGGGTGGGGCGGTGCGCGGCTTCTGATTTTAAAGAGGCATCTAGGGAATTGTCAGGCACCCT
ACAGGAAGGCCTGCCATGCTGTGGCCAACTGTTTCACTGGAGCAAGAAAGAGATCTCA

Alignment

ORF - retro_ggor_2792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 83.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  REVEILMFLSAIVMMKNRRSITVEQHIGNIFMFSKVANAILFFRLDIRMGLLYITLCIVFLMTCK----P
          REVEILMFLSAIVMMKNRRSITVEQHIGNIFMFSKVANAILFFRLDIRMGLLYITLCIVFLMTCK.....
Retrocopy REVEILMFLSAIVMMKNRRSITVEQHIGNIFMFSKVANAILFFRLDIRMGLLYITLCIVFLMTCKXXXXX

Parental  PLYMGP-EYIKYFNDKTIDEELERDKRVTWIVEFFANWSNDCQSFAPIYADLSLKYNCTGLNFGKVDVGR
          P.Y.GP.EYIKYFNDKT.DEELERD.RVTWIVEFFANWSNDCQSFAPIYADLSLKYNCTGLNFG.VD.GR
Retrocopy PMY-GP>EYIKYFNDKTTDEELERDNRVTWIVEFFANWSNDCQSFAPIYADLSLKYNCTGLNFGTVDAGR

Parental  YTDVSTRYKVSTSPLTKQLPTLILFQGGKEVMRRPQIDKKGRAVSWTFSEENVIREFNLNELYQRAKKLS
          YTDVSTRYKVSTSPLT.QLPTLILFQGGK.VMR.PQ.DKKGRAVSWTFSEENVI.EFNLNELYQRAKKLS
Retrocopy YTDVSTRYKVSTSPLTNQLPTLILFQGGKKVMRQPQTDKKGRAVSWTFSEENVI*EFNLNELYQRAKKLS

Parental  KAGDNIPEEQPVQ-PPP-QCQMGKTRRINKILTLAVLPLLSIPGAFHNHKPEATAFYLCFPFGCDWVGQR
          KAGDNIPEEQPV...PP.QCQ.GK.RRINKILTLAVLPLLSIPG.FHNHKPEATAFYLCFPFGCDWVG..
Retrocopy KAGDNIPEEQPVA>QPPPQCQTGKARRINKILTLAVLPLLSIPGSFHNHKPEATAFYLCFPFGCDWVGRC

Parental  AASDFKEASRELSGTLQEGLPCCGQLFRWSKKEIS
          AASDFKEASRELSGTLQEGLPCCGQLF.WSKKEIS
Retrocopy AASDFKEASRELSGTLQEGLPCCGQLFHWSKKEIS

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	6.71 RPM	69.10 RPM
SRP007412_cerebellum	6.11 RPM	51.38 RPM
SRP007412_heart	1.38 RPM	16.51 RPM
SRP007412_kidney	3.64 RPM	48.78 RPM
SRP007412_liver	2.00 RPM	29.04 RPM
SRP007412_testis	3.21 RPM	37.61 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2792 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2792 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035426	1 retrocopy	retro_cjac_3263,
Gorilla gorilla	ENSGGOG00000001519	1 retrocopy	retro_ggor_2792 ,
Monodelphis domestica	ENSMODG00000020112	1 retrocopy	retro_mdom_924,
Mus musculus	ENSMUSG00000050043	1 retrocopy	retro_mmus_154,