RetrogeneDB ID: retro_ggor_2156

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:20440323..20440719(+)
• Located in intron of: ENSGGOG00000000737

Retrocopy information

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

Parental gene information

• Parental gene symbol: DENR
• Ensembl ID: ENSGGOG00000005562
• Aliases: None
• Description: None

Sequence

>retro_ggor_2156
AATGAATTTGAAAAACTTACTGTACAAAATTCACCCAATCAAGAAGTGGAATTAGTAAGGGTCAAGGAATAGCAGGGGAA
GGGGAGAAGAAAAAACAGAAGAGAGGTGGAAGGGGTCAAATAAAACCAAAAAAGGAGACTGTACCATAAAAGGTTATTAT
AGCCAAAATTCCCAGAGCAAAGAAGAAATATGTAAAAACAGTGGGTGGCTTTGCAACTTTTGAAGTTGATCTTAAAGAAG
CACAAAGATTTTTCTGCTCAAAAATTCTCCTGTGGTACTTCAGTAACAGGGGAGGATGAAATTATTCAGGAAGACTCTAC
GGATGACATAATTGATATCATTCAGAAAAAACAGCCAGAGGTGGATGATGACAGCATCGAAGATCTTGAAGAAGTA

Alignment

ORF - retro_ggor_2156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.86 %
• Parental protein coverage: 67.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NEFAKLTVENSPKQE-AGISEGQGTAGEEEEKKKQKRDKGGRGQIKQKKKTVPQKVTIAKIPRAKKKYVT
          NEF.KLTV.NSP.QE..GIS.GQG.AGE.E.KKKQKR..GGRGQIK.KK.TVP.KV.IAKIPRAKKKYV.
Retrocopy NEFEKLTVQNSPNQE<SGISKGQGIAGEGE-KKKQKR--GGRGQIKPKKETVP*KVIIAKIPRAKKKYVK

Parental  RVCGLATFEIEIDLKEAQRFF-AQKFSCGASVTGEDEIIIQGDFTDDIIDVIQEKWPEVDDDSIEDLGEV
          .V.G.ATF..E.DLKEAQRFF.AQKFSCG.SVTGEDE.IIQ.D.TDDIID.IQ.K.PEVDDDSIEDL.EV
Retrocopy TVGGFATF--EVDLKEAQRFF>AQKFSCGTSVTGEDE-IIQEDSTDDIIDIIQKKQPEVDDDSIEDLEEV

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	10.93 RPM
SRP007412_cerebellum	0.00 RPM	7.84 RPM
SRP007412_heart	0.00 RPM	2.81 RPM
SRP007412_kidney	0.00 RPM	10.59 RPM
SRP007412_liver	0.03 RPM	4.93 RPM
SRP007412_testis	0.00 RPM	12.22 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_2156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2156 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1854
Pan troglodytes	retro_ptro_1236
Callithrix jacchus	retro_cjac_2627

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016012	1 retrocopy	retro_acar_71,
Bos taurus	ENSBTAG00000032433	1 retrocopy	retro_btau_110,
Callithrix jacchus	ENSCJAG00000020488	4 retrocopies	retro_cjac_1665, retro_cjac_2303, retro_cjac_2377, retro_cjac_2627,
Homo sapiens	ENSG00000139726	4 retrocopies	retro_hsap_1028, retro_hsap_1854, retro_hsap_2471, retro_hsap_4313,
Gorilla gorilla	ENSGGOG00000005562	3 retrocopies	retro_ggor_2156 , retro_ggor_2883, retro_ggor_813,
Nomascus leucogenys	ENSNLEG00000002186	3 retrocopies	retro_nleu_1465, retro_nleu_2136, retro_nleu_906,
Oryctolagus cuniculus	ENSOCUG00000008150	2 retrocopies	retro_ocun_1325, retro_ocun_1524,
Ochotona princeps	ENSOPRG00000015974	5 retrocopies	retro_opri_1000, retro_opri_1139, retro_opri_1147, retro_opri_133, retro_opri_183,
Pongo abelii	ENSPPYG00000005073	3 retrocopies	retro_pabe_1821, retro_pabe_3509, retro_pabe_861,
Pan troglodytes	ENSPTRG00000005584	4 retrocopies	retro_ptro_1236, retro_ptro_2921, retro_ptro_2955, retro_ptro_703,