RetrogeneDB ID: retro_ggor_2228

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:162735351..162736230(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOA1BP
• Ensembl ID: ENSGGOG00000000754
• Aliases: None
• Description: None

Sequence

>retro_ggor_2228
GGGGCGCGCCATGCGAGCAGGATGTCCGGTCTGCGGGCGCTGCCCGGGTCAGGCTGCTGGTTGCGGCTCGCGCCTGCGCG
AATCAAAAGCCAGACCAGCGCCTGCCGCTCGGGACCCACCTAGTGGGGACCGCAGCGGCTGAACTCGGGTGGCCGCTGGG
ACTCAGCGGTCATGGCGAGCATAGCGGTGAAGCACCTGAGCCAGGAGGAAGCCCAGGCCGTGGACCAGGAGCTATTCAAC
GAGTACTAGTTCAGCGTGGACCGACTTGTGGAGCTCGCCGGGCTGAGCTGTGCCGCAGCCATCGCCAAGGCATATTCCCC
CACGTCCGTGTCCAGGAGCTCCCCTACTGTCCTGGTCATCTGTGGCCCGGGGAATAATGGAGGAGATGGTCTGGTCTGTG
CTCCGCACCTCAAACTCTTTGGCTAACCAGCCAACCCTCTATTACCCCAAAAGGCCTAACAAGCCCCTCTTCATTGCGTT
GGTGACCCCGTGTCAGAAAATGGACATCCCTTTCCTTGGGGAAATGCGCTCAGAGCCCGTGATGATTGAGCTGTATGAGC
TGGTGGTGGATGTCATCTTCGGCTTCAGCTTCGAGGGTGATGTTCGGGAACGTTCCACAGCATCCTGAGTGTCCTGAAGG
GATTCACCGTGCCCACTGCCGGCATCAACATTCCCTCAGGATGGGATGTGGAGAAGGGAAACTTTGGAGGGATCTAGCCA
GACTTGCTCATCTCCCTCACGGCACCCAAAAAGTCTGCAACCCAGGTTACCCGGTCGCCACCATTACCTGGGGGGTCGTT
TTGTGCCACCTGTTCTGGAAAAGAAGTAGCACCTGAACCTGCCCCCTACCCTGACACCAAGTGTGTGTATGGTCTGCAG

Alignment

ORF - retro_ggor_2228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.45 %
• Parental protein coverage: 98.01 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GARSASWMSGLRALLGFG-LLVAS-SRL-PRVKSQTIACRSGPTWWGPQRLNSGGRWDSEVMASTAVKYL
          GAR.AS.MSGLRAL.G.G.LLVA..SRL..R.KSQT.ACRSGPT.WGPQRLNSGGRWDS.VMAS.AVK.L
Retrocopy GARHASRMSGLRALPGSG<LLVAA<SRL<ARIKSQTSACRSGPT*WGPQRLNSGGRWDSAVMASIAVKHL

Parental  SQEEAQAVDQELFNEYQFSVDQLMELAGLSCATAIAKAYPPTSMSRSPPTVLVICGPGNNGGDGLVCARH
          SQEEAQAVDQELFNEY.FSVD.L.ELAGLSCA.AIAKAY.PTS.SRS.PTVLVICGPGNNGGDGLVCA.H
Retrocopy SQEEAQAVDQELFNEY*FSVDRLVELAGLSCAAAIAKAYSPTSVSRSSPTVLVICGPGNNGGDGLVCAPH

Parental  LKLFG-YEPTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPAEPMTIDELYELVVDAIFGFSFKGDVRE-
          LKLFG...PT.YYPKRPNKPLF.ALVT.CQKMDIPFLGEM..EP..I.ELYELVVD.IFGFSF.GDVRE.
Retrocopy LKLFG>NQPTLYYPKRPNKPLFIALVTPCQKMDIPFLGEMRSEPVMI-ELYELVVDVIFGFSFEGDVRE<

Parental  PFHSILSVLKGLTVPIASIDIPSGWDVEKGNAGGIQPDLLISLTAPKKSATQFT-GRYHYLGGRFVPPAL
          .FHSILSVLKG.TVP.A.I.IPSGWDVEKGN.GGI.PDLLISLTAPKKSATQ.T.GR.HYLGGRFVPP.L
Retrocopy TFHSILSVLKGFTVPTAGINIPSGWDVEKGNFGGI*PDLLISLTAPKKSATQVT>GRHHYLGGRFVPPVL

Parental  EKKYQLNLP-PYPDTECVYRLQ
          EKK..LNLP.PYPDT.CVY.LQ
Retrocopy EKK*HLNLP<PYPDTKCVYGLQ

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	41.96 RPM
SRP007412_cerebellum	0.39 RPM	20.80 RPM
SRP007412_heart	0.13 RPM	23.98 RPM
SRP007412_kidney	0.04 RPM	45.26 RPM
SRP007412_liver	0.08 RPM	27.30 RPM
SRP007412_testis	0.21 RPM	12.12 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_2228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2228 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3275
Pan troglodytes	retro_ptro_2215
Pongo abelii	retro_pabe_2709
Macaca mulatta	retro_mmul_2060

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000163382	2 retrocopies	retro_hsap_1973, retro_hsap_3275,
Gorilla gorilla	ENSGGOG00000000754	1 retrocopy	retro_ggor_2228 ,
Macaca mulatta	ENSMMUG00000002623	2 retrocopies	retro_mmul_1364, retro_mmul_2060,
Nomascus leucogenys	ENSNLEG00000012663	2 retrocopies	retro_nleu_2615, retro_nleu_2992,
Pongo abelii	ENSPPYG00000000713	2 retrocopies	retro_pabe_1692, retro_pabe_2709,
Pan troglodytes	ENSPTRG00000001463	2 retrocopies	retro_ptro_1315, retro_ptro_2215,