RetrogeneDB ID: retro_ggor_2883

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:110808196..110808570(-)
• Located in intron of: ENSGGOG00000012871

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_2883
TCACCCAAACAAGAAGCTGGAATTAATGAGGGTCAAGGAACAGCAGGGGCAGAAGAGGAGAATAAAATACAAAAGAGAGG
TGAAAGGGGTCAAATAAAACAAAGAAAAGAAGGCCATACCAGAAAAGGTTACACAGCCTAAATTCCCAGAACAGAGAAGA
AACATGTAACATGAATGTGTGGCCTCTAACTTTTGAAATTGATCTTAAAAAAGCACAAAGATTTTTTGCTCAAAAATTGT
GTAGTGCCTCAGTAACAGAAGAGGAAGAAATTATCATTCAGGAAGACTTTACAGATGACGTAATTGATGTTATTCAGGAA
AACTGGCCAGAGGTAAATGATGACAGCATTGAAGATCTTGGAGAGGTAAAGAAG

Alignment

ORF - retro_ggor_2883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 63.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SPKQEAGISEGQGTAGEEEEKKKQKRDKGGRGQIKQKK-KTVPQKVTIAK-IPRAKKKYVTRVCGL-ATF
          SPKQEAGI.EGQGTAG.EEE.K.QKR..G.RGQIKQ.K.K..P.KVT..K.IPR..KK.VT..CGL..TF
Retrocopy SPKQEAGINEGQGTAGAEEENKIQKR--GERGQIKQRK>KAIPEKVTQPK<IPRTEKKHVT*MCGL<LTF

Parental  EIEIDLKEAQRFFAQKFSCGASVTGEDEIIIQGDFTDDIIDVIQEKWPEVDDDSIEDLGEVKK
          EI..DLK.AQRFFAQK..C.ASVT.E.EIIIQ.DFTDD.IDVIQE.WPEV.DDSIEDLGEVKK
Retrocopy EI--DLKKAQRFFAQKL-CSASVTEEEEIIIQEDFTDDVIDVIQENWPEVNDDSIEDLGEVKK

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	0.00 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_2883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2883 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4313
Pan troglodytes	retro_ptro_2921

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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,