RetrogeneDB ID: retro_ggor_2219

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:139416453..139417316(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OBFC1
• Ensembl ID: ENSGGOG00000008979
• Aliases: None
• Description: None

Sequence

>retro_ggor_2219
ACTGGAGTTATAAACTGCATCTGCTAGAAAATATTGAGCAATATCAAGTTTTCATCCGCTGCTCCAAATGCAGCAAGAGA
ACTGAGCTTTACCTCAATACTCAAGAAGCTTCAAGACACCATTGAGCAGAGAACAAAAATTGAAACTGGGGACATGTTCT
GAATCAGAGGCTATGTCTACACATGCAGAGAAGAGTGAGAAATGTATGCCACTGCTTATTATAAAGTGGACGATCCAGTG
TGGAACATTCAAATTGCAAGGGTGTTTGAGCTGCCCATTAATCTACAGGAAAGTTTAGACCAAGCCTTTCCATTGCCCAG
ACTTAGAGAAAGAAGAAGCACTAAGCAATCCAGGTGTCCTGGCCTTCACTAGTCTCATGTGTTTGCTGAGTGAAAAAGCC
AAAGAATTCCCCATGAAGAACAGAGTGCAGACCTTTGACCAGCAGGAGTTGGAAATGGTGGAGCCTTTGCCGTCCCTTGC
TAACCAGCCTGTTACTGACAGTGCCTGCTCTGAACAAGGAAATTTTAAGAAGGATATCACTTTCAAGGCAATTTATAGCA
TATTTTAAAATGCTATTCAACAGCTGCAGGAAAAAGGACTCGTTTTCCAGAAAGATGGTGGTTTTGATAACCTATGCTGT
GTAACCAGAAAAGACAAAGACCTGTATAGGAAAATCCACTGGATAATTCAGGAAGACTACCAGAAACCAAATCACCCGAA
GAAGGGCTGCCGCTTCCTGCACATCTTGGCCTGCGCTCACCCTGAGCATCTGCCCAGTTCTAGGTAGGGCTATGTTGCAG
CAACTTCTGGAGCTCCTGGAGGACCAGAGTGACCTCATCAGCACAATGGAGCACCACTACTCC

Alignment

ORF - retro_ggor_2219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.36 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIEQRTKIEIGDTIRVRGSIRTYREEREIHA
          TGVINCIC.K.L.N....SAAP.AARELS.TS.LKKLQ.TIEQRTKIE.GD....RG...T.REE.E..A
Retrocopy TGVINCIC*KILSNIKFSSAAPNAARELSFTSILKKLQDTIEQRTKIETGDMF*IRGYVYTCREE*EMYA

Parental  TAYYKVDDPVWNIQIARMLELPT-IYRKVYDQPFHSSALEKEEALSNPGALDLPSLTSLLSEKAKEFLME
          TAYYKVDDPVWNIQIAR..ELP..IYRKV...PFH...LEKEEALSNPG.L...SL..LLSEKAKEF.M.
Retrocopy TAYYKVDDPVWNIQIARVFELPI>IYRKV*TKPFHCPDLEKEEALSNPGVLAFTSLMCLLSEKAKEFPMK

Parental  NRVQSFYQQELEMVESLLSLANQPVIHSACSDQVNFKKDTTSKAIHSIFKNAIQLLQEKGLVFQKDDGFD
          NRVQ.F.QQELEMVE.L.SLANQPV..SACS.Q.NFKKD.T.KAI.SIF.NAIQ.LQEKGLVFQKD.GFD
Retrocopy NRVQTFDQQELEMVEPLPSLANQPVTDSACSEQGNFKKDITFKAIYSIF*NAIQQLQEKGLVFQKDGGFD

Parental  NLYYVTREDKDLHRKIHRIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDI
          NL..VTR.DKDL.RKIH.IIQ.D.QKPNH..KGC.FLHILACA..LSI.P.L..A.LQQ.LELLEDQSD.
Retrocopy NLCCVTRKDKDLYRKIHWIIQEDYQKPNHPKKGCRFLHILACAH>LSICPVLGRAMLQQLLELLEDQSDL

Parental  VSTMEHYYT
          .STMEH.Y.
Retrocopy ISTMEHHYS

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	6.67 RPM
SRP007412_cerebellum	0.00 RPM	9.69 RPM
SRP007412_heart	0.00 RPM	4.69 RPM
SRP007412_kidney	0.00 RPM	14.72 RPM
SRP007412_liver	0.00 RPM	8.28 RPM
SRP007412_testis	0.00 RPM	41.96 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_2219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2219 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3257
Pan troglodytes	retro_ptro_2203
Pongo abelii	retro_pabe_2701
Macaca mulatta	retro_mmul_2050
Callithrix jacchus	retro_cjac_1791

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018342	1 retrocopy	retro_cjac_1791,
Homo sapiens	ENSG00000107960	1 retrocopy	retro_hsap_3257,
Gorilla gorilla	ENSGGOG00000008979	1 retrocopy	retro_ggor_2219 ,
Macaca mulatta	ENSMMUG00000015323	1 retrocopy	retro_mmul_2050,
Nomascus leucogenys	ENSNLEG00000015282	1 retrocopy	retro_nleu_2689,
Pongo abelii	ENSPPYG00000002628	1 retrocopy	retro_pabe_2701,
Pan troglodytes	ENSPTRG00000002919	1 retrocopy	retro_ptro_2203,