RetrogeneDB ID: retro_ggor_1229

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 16:24142472..24143399(+)
• Located in intron of: ENSGGOG00000004218

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000216671
• Ensembl ID: ENSGGOG00000008136
• Aliases: None
• Description: None

Sequence

>retro_ggor_1229
ACTGCTGTGGAGCCTGCCCAGTCGGATTTAGGAGCCCGCAAGGGCCATGACCTGCAGCACATCAGCGACCAGGAGATGCC
CAAATATTTTGCTTCTGACCATCCAAGGGAAAGTACACTTTTTTTGAGAAAATATCAAATGAGTGTGCAAGAAAAGAGGA
GGAGCTCTCATCTATAGTATATACCCCCATGGCATCTTGATAGAAAATACACCTCGTGTTACACCATATTGCTAGATAAC
AGAACAGTCAGCCAGCCTGATCTTTGACACACATTAGAAAGTGTGACTTAGGCAATATATTACAACATAAAGCACAGATA
CGCAAATAGATCTCTGGCTATTTTTGACAAGCCAGTACACCCACTTTCACAAGAGAAGTTTCCAGGGAAATCCTTCGAGC
ATGATCCCAAACGCAACTGTACTTTCAGATATTTCTGTACTCTTTTTCAAGTCATAAAACTAACAGCTCCATGTGCAATC
GTAGCTTTGGTGTACATCGAACGACTTTTAACTAATGGTAGCATCGCTCTTTGTCCTACTAATTGGAAAAAGATTGTGCT
CGGAGCCATGCTTCTTGCCTCCAAGGTTTGGAGAAATCATGGTCTGTGGAGTGTGGATGACAGCCAGAATCCCAAGGACA
TTGCAGTTGAGAACATGAGCAAGATGGAGAAGTGTTTTTTGGAGCTACTTGGGTTTAATATTCATGTGTCTGCCAGTGTT
TATGCAAGATATTACTTCGACCTGTGTGCCTTGGCAAATGACCGTGACCTGTATTTTCTATTTAGTTTTCTTCACAAAGA
TAAAGCACAGAAACTGGAGGCTGTGTCATGGCCGTGTGAATACAAAGACTTGCATCAACATGCCGCTGCTATAACAAGGG
CTATCAGCATGAATTTCATTGGTATTCGGTGCACTAATGCCATCTTA

Alignment

ORF - retro_ggor_1229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.57 %
• Parental protein coverage: 92.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAVEPAQSDFGAREGHDLQHISDQQMPKNFASDRPRESTLFLRKYQMSAVRNEKRSSSHLYYIPACHLDR
          TAVEPAQSD.GAR.GHDLQHISDQ.MPK.FASD.PRESTLFLRKYQMS....EKR.SSHL.YIP..HLDR
Retrocopy TAVEPAQSDLGARKGHDLQHISDQEMPKYFASDHPRESTLFLRKYQMSV--QEKRRSSHL*YIPPWHLDR

Parental  KYSSCSTILLDNSTASQPDLRHTLESVALAIYYNIKHSYANRSLAIFEEPIHPLSQEKLPGKSFKHDPKH
          KY.SC.TILLDN.T.SQPDL.HTLESV..AIYYNIKH.YANRSLAIF..P.HPLSQEK.PGKSF.HDPK.
Retrocopy KYTSCYTILLDNRTVSQPDL*HTLESVT*AIYYNIKHRYANRSLAIFDKPVHPLSQEKFPGKSFEHDPKR

Parental  NCIFRYFCTLFQVIKLTAPCAIVALVYIERLLTSANIDLCPTNWKKIVLGTMLLASKVWRNRGLWSVDDS
          NC.FRYFCTLFQVIKLTAPCAIVALVYIERLLT...I.LCPTNWKKIVLG.MLLASKVWRN.GLWSVDDS
Retrocopy NCTFRYFCTLFQVIKLTAPCAIVALVYIERLLTNGSIALCPTNWKKIVLGAMLLASKVWRNHGLWSVDDS

Parental  QNPKDTAVENMSKMEKCFLELLEFNIHVSASVYAKYYFDLHALANDHDLYFLFSFLHKDKAQKLEAMSRL
          QNPKD.AVENMSKMEKCFLELL.FNIHVSASVYA.YYFDL.ALAND.DLYFLFSFLHKDKAQKLEA.S..
Retrocopy QNPKDIAVENMSKMEKCFLELLGFNIHVSASVYARYYFDLCALANDRDLYFLFSFLHKDKAQKLEAVSWP

Parental  CEYKDLHQDAAALKRVISMNFIGIGCSNAIL
          CEYKDLHQ.AAA..R.ISMNFIGI.C.NAIL
Retrocopy CEYKDLHQHAAAITRAISMNFIGIRCTNAIL

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	0.24 RPM	0.00 RPM
SRP007412_cerebellum	0.59 RPM	0.00 RPM
SRP007412_heart	0.06 RPM	0.00 RPM
SRP007412_kidney	0.29 RPM	0.00 RPM
SRP007412_liver	0.13 RPM	0.00 RPM
SRP007412_testis	1.14 RPM	5.28 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_1229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1229 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1629
Pongo abelii	retro_pabe_1345

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011445	1 retrocopy	retro_cjac_1164,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Gorilla gorilla	ENSGGOG00000008136	1 retrocopy	retro_ggor_1229 ,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,
Pan troglodytes	ENSPTRG00000008072	1 retrocopy	retro_ptro_1091,