RetrogeneDB ID: retro_ggor_2790

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:36177963..36178414(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND6
• Ensembl ID: ENSGGOG00000015621
• Aliases: None
• Description: None

Sequence

>retro_ggor_2790
AGCCAACCTGCAACCTCGGAATCTTTACCAGTTCGATGCACAGATGGCAGTGTCCCAGAAGCCCAGTCAACATCTTCATC
TATGCAGCCAAGCCCTGTATCAAATCAGTCACTTTTATCAGAATCTGTAGCATCTTCCCAATTGGACAGTACATCTGTGG
ACAAGCAGTACCTGAAACAGAAGATCTGCGGGCTTCAGTATCAGACATGGCACAGCAGCCATCTGAAGAGCAAAGCAAGT
CTCTTGAAAAACCAAAACAAAAAAAGAATCTCTGTTTCATGTGCAGGAAGAAAGTGGGACTTACTGGGTTTGAACGCGGT
GTAGAAATGTTTACTGTGGTGTACACTATTACTCAGATCTACACAATTGCTTTTAAAATTACAAAGCTGATGCCACTGAG
AAAATCAGAAAAGAAAATCCAGTAGTTGTTGGCGAGAAGATCCAAAAGATT

Alignment

ORF - retro_ggor_2790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.53 %
• Parental protein coverage: 73.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVSSLSESLPVQCTDGSVPEAQSTLDSTSSSMQPSPVSNQSLLSESVASSQLDSTSVDK-AVPETEDVQA
          S....SESLPV.CTDGSVPEAQ....STSSSMQPSPVSNQSLLSESVASSQLDSTSVDK.AVPETED..A
Retrocopy SQPATSESLPVRCTDGSVPEAQ----STSSSMQPSPVSNQSLLSESVASSQLDSTSVDK<AVPETEDLRA

Parental  SVSDTAQQPSEEQSKSLEKPKQKKNRCFMCRKKVGLTGFE-CRCGNVYCGVHRYSDVHNCSYNYKADAAE
          SVSD.AQQPSEEQSKSL.......N.CFMCRKKVGLTGFE..RC.NVYCGVH.YSD.HNC..NYKADA.E
Retrocopy SVSDMAQQPSEEQSKSLXXXXXXXNLCFMCRKKVGLTGFE<TRCRNVYCGVHYYSDLHNCF*NYKADATE

Parental  KIRKENPVVVGEKIQKI
          KIRKENPVVVGEKIQKI
Retrocopy KIRKENPVVVGEKIQKI

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	12.32 RPM
SRP007412_cerebellum	0.04 RPM	16.94 RPM
SRP007412_heart	0.00 RPM	9.10 RPM
SRP007412_kidney	0.00 RPM	42.97 RPM
SRP007412_liver	0.03 RPM	29.25 RPM
SRP007412_testis	3.73 RPM	90.34 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_2790 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2790 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4153
Pan troglodytes	retro_ptro_2824

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012321	1 retrocopy	retro_btau_593,
Choloepus hoffmanni	ENSCHOG00000009491	2 retrocopies	retro_chof_1516, retro_chof_2072,
Felis catus	ENSFCAG00000012931	2 retrocopies	retro_fcat_1024, retro_fcat_1998,
Homo sapiens	ENSG00000086666	1 retrocopy	retro_hsap_4153,
Gorilla gorilla	ENSGGOG00000008957	1 retrocopy	retro_ggor_1485,
Gorilla gorilla	ENSGGOG00000015621	1 retrocopy	retro_ggor_2790 ,
Loxodonta africana	ENSLAFG00000006722	1 retrocopy	retro_lafr_587,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685,
Nomascus leucogenys	ENSNLEG00000008870	1 retrocopy	retro_nleu_1387,
Pan troglodytes	ENSPTRG00000007361	2 retrocopies	retro_ptro_1375, retro_ptro_2824,
Rattus norvegicus	ENSRNOG00000013506	1 retrocopy	retro_rnor_2019,
Sus scrofa	ENSSSCG00000001779	2 retrocopies	retro_sscr_1206, retro_sscr_1207,