RetrogeneDB ID: retro_ggor_3023

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:63259162..63259725(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN7L3
• Ensembl ID: ENSGGOG00000010959
• Aliases: None
• Description: None

Sequence

>retro_ggor_3023
AAGAACCCCGATTCCCCTTGAAGATCTGAGTCTTTAAAACACAAAAATGGGGAACTTTGTGATTTGATTTTTTTTAAGTA
TAACAACTCAACTGGGATCAGCTACGAAACCTGGGGCCAGAGGAGCTTCATATCCTGCTAAGCATGCAATGTAGGGTGAT
TTCTGAAGATACCAAGAAGATGTGCACAAAGTCCCTGCACTGCCCACAGCACACAGTTGAGCAGAAGTGAACCTTGCAGA
TGTATTTCTTCAGGGCCTCAGCTGTCCATCCAGAGGTGGAGAGCTCCCAGGATAATGACAGCTTTGACATGACTGACAGC
CAGGCCCTGATCAGCCAGCTTCAGTGGGTCTGCTCCTCTGATCTCTCACCCTGTGATTCAGGCTCCCCCAAGACGAGCGA
AAATCAGGGATGGGGTCTAGGTACCAACAGCTCTGAGACACAGAAAACCAAGAAAAAGAAATCCCATCTGAGCCTGGTAG
GGACTTCCTCCGACCTGGGCTCCAACAGGAAGAAGCCAAAGCTACCGATACCCCCGACGGCCAGCATCTATGATGACATC
AAC

Alignment

ORF - retro_ggor_3023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.84 %
• Parental protein coverage: 53.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QNPNSPRRSKSLKHKNGELSNSDPFKYNNSTGISYET-LGPEELRSLLTTQCGVISEHTKKMCTRSLRCP
          .NP.SP.RS.SLKHKNGEL......KYNNSTGISYET.LGPEEL..LL..QC.VISE.TKKMCT.SL.CP
Retrocopy KNPDSP*RSESLKHKNGELCDLXXXKYNNSTGISYET<LGPEELHILLSMQCRVISEDTKKMCTKSLHCP

Parental  QHTDEQRRTVRIYFLGPSAVLPEVESSLDNDSFDMTDSQALISRLQWDGSSDLSPSDSGSSKTSENQGWG
          QHT.EQ..T...YF...SAV.PEVESS.DNDSFDMTDSQALIS.LQW..SSDLSP.DSGS.KTSENQGWG
Retrocopy QHTVEQK*TLQMYFFRASAVHPEVESSQDNDSFDMTDSQALISQLQWVCSSDLSPCDSGSPKTSENQGWG

Parental  LGTNSSESRKTKKKKSHLSLVGTASGLGSNKKKKPKPPAPPTPSIYDDIN
          LGTNSSE..KTKKKKSHLSLVGT.S.LGSN..KKPK.P.PPT.SIYDDIN
Retrocopy LGTNSSETQKTKKKKSHLSLVGTSSDLGSN-RKKPKLPIPPTASIYDDIN

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	0.00 RPM	200.88 RPM
SRP007412_cerebellum	0.00 RPM	80.92 RPM
SRP007412_heart	0.00 RPM	13.95 RPM
SRP007412_kidney	0.00 RPM	28.83 RPM
SRP007412_liver	0.00 RPM	18.12 RPM
SRP007412_testis	0.00 RPM	67.55 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_3023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3023 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4847

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003379	13 retrocopies	retro_dnov_1026, retro_dnov_1144, retro_dnov_1211, retro_dnov_1590, retro_dnov_1902, retro_dnov_2325, retro_dnov_2448, retro_dnov_2497, retro_dnov_2600, retro_dnov_516, retro_dnov_86, retro_dnov_867, retro_dnov_961,
Homo sapiens	ENSG00000087152	1 retrocopy	retro_hsap_4847,
Gorilla gorilla	ENSGGOG00000010959	1 retrocopy	retro_ggor_3023 ,
Myotis lucifugus	ENSMLUG00000006416	1 retrocopy	retro_mluc_41,
Macaca mulatta	ENSMMUG00000029935	1 retrocopy	retro_mmul_820,