RetrogeneDB ID: retro_ggor_2470

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:127922449..127922779(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH4
• Ensembl ID: ENSGGOG00000005708
• Aliases: None
• Description: None

Sequence

>retro_ggor_2470
GAGGACATGGTCTCTGTCTTCTTTCTCCTCAGTTGCAGGCTCATTTTTCTCTCAGTCTTCATAATTACATTGTCTGATTT
AGAGTGTGATTACATTAATGCTAGATCATGTTGCTCAACATTAAACAAGTGGGTAATTTCCAAGATTGATTGGCCATACT
ATTGTCACTGTATTATGCGCATTTTGTTGCACTGGTTCATCTTCCTTCTCAACTTACCTCTTGCCACTTGGAATATATAT
TGATTCATTATGGTGCCAAGCAGTAACGTAGGAGTGTTTGATCCAACAGAAATACACAATCAAGGACAGCAAAAGTAACA
CATGAAAGAC

Alignment

ORF - retro_ggor_2470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 80.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EAVVFVFSLLDCCALIFLSVYFIITLSDLECDYINARSCCSKLNKWVI-PELIGHTIVTVL-LLISLHWF
          E..V.VF.LL.C..LIFLSV.FIITLSDLECDYINARSCCS.LNKWVI.P.LIGHTIVTVL...I.LHWF
Retrocopy EDMVSVFFLLSC-RLIFLSV-FIITLSDLECDYINARSCCSTLNKWVI>PRLIGHTIVTVL<MRILLHWF

Parental  IFLLNLPVATWNIYRYIMVPSGNMGVFDPTEIHNRGQLKSHMKE
          IFLLNLP.ATWNIY..IMVPS.N.GVFDPTEIHN.GQ.K.HMK.
Retrocopy IFLLNLPLATWNIY*FIMVPSSNVGVFDPTEIHNQGQQK*HMKD

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	9.06 RPM
SRP007412_cerebellum	0.00 RPM	7.68 RPM
SRP007412_heart	0.00 RPM	4.16 RPM
SRP007412_kidney	0.00 RPM	16.52 RPM
SRP007412_liver	0.00 RPM	9.71 RPM
SRP007412_testis	0.00 RPM	16.68 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_2470 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2470 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006544	1 retrocopy	retro_chof_327,
Callithrix jacchus	ENSCJAG00000008013	1 retrocopy	retro_cjac_2474,
Cavia porcellus	ENSCPOG00000007310	1 retrocopy	retro_cpor_777,
Dasypus novemcinctus	ENSDNOG00000007093	1 retrocopy	retro_dnov_1669,
Homo sapiens	ENSG00000143771	1 retrocopy	retro_hsap_3656,
Gorilla gorilla	ENSGGOG00000005708	1 retrocopy	retro_ggor_2470 ,
Myotis lucifugus	ENSMLUG00000003134	1 retrocopy	retro_mluc_1314,
Macaca mulatta	ENSMMUG00000009936	1 retrocopy	retro_mmul_1796,
Nomascus leucogenys	ENSNLEG00000013549	1 retrocopy	retro_nleu_514,
Ochotona princeps	ENSOPRG00000001589	1 retrocopy	retro_opri_749,
Pongo abelii	ENSPPYG00000000183	1 retrocopy	retro_pabe_3003,
Pan troglodytes	ENSPTRG00000002025	1 retrocopy	retro_ptro_2481,
Pteropus vampyrus	ENSPVAG00000014034	1 retrocopy	retro_pvam_692,
Ictidomys tridecemlineatus	ENSSTOG00000027396	2 retrocopies	retro_itri_1502, retro_itri_1552,
Vicugna pacos	ENSVPAG00000012521	2 retrocopies	retro_vpac_180, retro_vpac_215,