RetrogeneDB ID: retro_ggor_3030

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:68682745..68683401(-)
• Located in intron of: ENSGGOG00000015672

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000100836
• Ensembl ID: ENSGGOG00000022683
• Aliases: None
• Description: None

Sequence

>retro_ggor_3030
CCTGGTTCGGGAGCCCCTGGCAGCCAAGAGGAGGAGGAGGAGCCATGACTGGTCGAGGGTGACCCGGAAGACAGCGCCAT
TGAGGATCCGGAGCTGGAAGCTATCAAAGCTCGAGTTAGGGAGATGGAGGAAGAAGCTGAGAAGCTAAAGGAGCTACAGA
TCGAGGTAGAGAAGCAGATGAGTATGAGTCCACCTCCAGGAAATGCTGGCCCAATGATCATGTCATCGAGGAGAAGATGG
AGGCCGATGCCCGTTCCGTCTATGTTGGCAATGTTGACTATGGTGCAACAGCAGAAGAGCTGGAAGCTCACTTTCATGGC
TGTGGTTTAGTCAACTGTGTTACCATACTCTGTGACAAATTTAGTGGCCATCCCAAAGGGTTTGCATATATAGAGTTCTC
AGACAAAGAGTCAGTGAGGACTTCCCTGGCCTTAGATGACTCCCTATTTAGAGGAAGGCAAATCAAGGTGATCCCAAAAT
GAACCAACAGACCAGGAATCAGCACAACAGATCGGGGTTTTCCACGAGCCCGCTACCGTGCCCGGACCACCAACTACAAC
AGTTCCCTCTCTCGATTCCACAGTGGTTTTAACAGCAGGCCCCGGGGTCACGTCTACAGAGGCCAGGCTAGAGCGACATC
ATGGTACTCCCCTTAC

Alignment

ORF - retro_ggor_3030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.73 %
• Parental protein coverage: 77.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGSGAPGSQEEEEEPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAG
          PGSGAPGSQEEEEEP.LVEGDP.D.AIEDPELEAIKARVREMEEEAEKLKELQ.EVEKQM.MSPPPGNAG
Retrocopy PGSGAPGSQEEEEEP*LVEGDPEDSAIEDPELEAIKARVREMEEEAEKLKELQIEVEKQMSMSPPPGNAG

Parental  PVIMS-IEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV
          P.IMS.IEEKMEADARS.YVGNVDYGATAEELEAHFHGCG.VN.VTILCDKFSGHPKGFAYIEFSDKESV
Retrocopy PMIMS<IEEKMEADARSVYVGNVDYGATAEELEAHFHGCGLVNCVTILCDKFSGHPKGFAYIEFSDKESV

Parental  RTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRVYRGR
          RTSLALD.SLFRGRQIKVIPK.TNRPGISTTDRGFPRARYRARTTNYNSS.SRF.SGFNSRPRG.VYRG.
Retrocopy RTSLALDDSLFRGRQIKVIPK*TNRPGISTTDRGFPRARYRARTTNYNSSLSRFHSGFNSRPRGHVYRGQ

Parental  ARATSWYSPY
          ARATSWYSPY
Retrocopy ARATSWYSPY

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	0.43 RPM	107.32 RPM
SRP007412_cerebellum	0.43 RPM	146.36 RPM
SRP007412_heart	0.28 RPM	34.65 RPM
SRP007412_kidney	0.25 RPM	105.33 RPM
SRP007412_liver	0.24 RPM	48.09 RPM
SRP007412_testis	0.21 RPM	105.57 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_3030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3030 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4855
Pan troglodytes	retro_ptro_3232
Macaca mulatta	retro_mmul_2594

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263, retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030 ,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645, retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339, retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625,