RetrogeneDB ID: retro_ggor_2092

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:37374456..37375289(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX56
• Ensembl ID: ENSGGOG00000012031
• Aliases: None
• Description: None

Sequence

>retro_ggor_2092
GGAGTAAGTCTCTGCTCTTTGTCAACTCTAGAATGGAGTTACTGGCTACACCTGTTTCTGGAGCAGTTCAGCATCTCCAC
CTGTGTGCTCAATGGAGCACTTCCCCTGCTCTCCAGGTGCCACATCATCTCACAGTTCAACCAAGGCTTCTAGGACTGTG
TCATAGCAACTGATGCTGAAGTCCTGGGGGCCCCAGTCAAGGGCAAGCGTCAGGGCGAGGGGCCAAAGCGGACAAGGCCT
CTAATATGGAGGCAGGTGTGGCCCGGGGCATAGACTTCCACTATGTGTCTGCTGTGCTCAACTTTGATCTTCCCCCCACC
CCCGAGGCCTACATCCATCAAACCGGCAGGACAGTGTGCTACAATCCAGGCATAGTCTTAACCTTTGTGTTGCCCAGGGA
ACAGTCCCACTTGGGCAAGATTGAGGACCTTCTCAGTGAAGAGAACAAGGGCCCCATCCTGCTCCCCTACCAGTTCCGGA
TGGAGAAGATTGAGGGCTTCCGCTATCGCTGCAGGGATGCCATGTGCTCAGTGGCTAAACAGGCCATTCGAGAGGTGAGA
TTGAAGGAGATCAAGGAGGAGCTTCTGCACTCTAAGAAGCTCAAGATGTACTTTGAAGACAACCCTAGGGACCTCCAGGT
GCTGCAGCATGACCTGCCGTTGCACCCCGCGGTGGTGAAGCCCCACCTGGGCCATGTTCCTGACTACCTGGTTCCTACTG
CTCTCCATGGCCTGGTGCACCCTCACAAGAAGCGGAAGAAGCTGTCTTCCTCTCATAGGAAGGCCAAGAGAGCAAAGTCC
CAGAACCCACTGCACAGTTTCAAGCACAAAGGA

Alignment

ORF - retro_ggor_2092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.64 %
• Parental protein coverage: 51.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKSLLFVNTLERSYRLRLFLEQFSIPTCVLNGELPLRSRCHIISQFNQGFYDCVIATDAEVLGAPVKGKR
          G.SL....TLE.SY.L.LFLEQFSI.TCVLNG.LPL.SRCHIISQFNQGF.DCVIATDAEVLGAPVKGKR
Retrocopy GVSLCSLSTLEWSYWLHLFLEQFSISTCVLNGALPLLSRCHIISQFNQGF*DCVIATDAEVLGAPVKGKR

Parental  RGRGPK-GDKASDPEAGVARGIDFHHVSAVLNFDLPPTPEAYIHRAGRTARANNPGIVLTFVLPTEQFHL
          .G.GPK..DKAS..EAGVARGIDFH.VSAVLNFDLPPTPEAYIH..GRT....NPGIVLTFVLP.EQ.HL
Retrocopy QGEGPK<ADKASNMEAGVARGIDFHYVSAVLNFDLPPTPEAYIHQTGRTV-CYNPGIVLTFVLPREQSHL

Parental  GKIEELLSGENRGPILLPYQFRMEEIEGFRYRCRDAMRSVTKQAIREARLKEIKEELLHSEKLKTYFEDN
          GKIE.LLS.EN.GPILLPYQFRME.IEGFRYRCRDAM.SV.KQAIRE.RLKEIKEELLHS.KLK.YFEDN
Retrocopy GKIEDLLSEENKGPILLPYQFRMEKIEGFRYRCRDAMCSVAKQAIREVRLKEIKEELLHSKKLKMYFEDN

Parental  PRDLQLLRHDLPLHPAVVKPHLGHVPDYLVPPALRGLVRPHKKRKKLSSSCRKAKRAKSQNPLRSFKHKG
          PRDLQ.L.HDLPLHPAVVKPHLGHVPDYLVP.AL.GLV.PHKKRKKLSSS.RKAKRAKSQNPL.SFKHKG
Retrocopy PRDLQVLQHDLPLHPAVVKPHLGHVPDYLVPTALHGLVHPHKKRKKLSSSHRKAKRAKSQNPLHSFKHKG

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	32.18 RPM
SRP007412_cerebellum	0.04 RPM	53.58 RPM
SRP007412_heart	0.00 RPM	11.88 RPM
SRP007412_kidney	0.08 RPM	36.43 RPM
SRP007412_liver	0.00 RPM	29.78 RPM
SRP007412_testis	0.00 RPM	35.33 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_2092 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2092 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000012031	1 retrocopy	retro_ggor_2092 ,
Pan troglodytes	ENSPTRG00000019147	1 retrocopy	retro_ptro_211,