RetrogeneDB ID: retro_ggor_1316

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:80682814..80683176(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS23
• Ensembl ID: ENSGGOG00000025014
• Aliases: None
• Description: None

Sequence

>retro_ggor_1316
CTTCGTACCAAGAATCTCCCTGTTCACTGACAGGAACAGAAGTGGAATGACAAACAGTACAAGAAAGCCCATTTAGGCAC
AGCCTGAAGGCCAACGCTTTTGGAAATGCTTCCCATACAAAGAGAACTGTGTTGGAAAAATAGGAGTTGAAGCCGAATGG
CCAAATTCTAATATCAGGAAGTGTACTATAGTTCAGCTGATTGAGAATGGCAAGAAAATCATAGTCTTTGTACCCAACGA
TGGTTGCTTGAACTTTATTGAGGAAAAGATGAATTTCTGGTTGCTGAATTGGTCAAAAAGGTGGTACTGTTGTTGACATT
CCTGTAGTCCGCTTTAATGTTGTCAGAGTAGCCAGTGTCTCT

Alignment

ORF - retro_ggor_1316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.29 %
• Parental protein coverage: 86.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LRTARKLRSHRRDQKWHDKQYKKAHLGTA-LKANPFGGASHAKGIVLEK-VGVEAKQPNSAIRKCVRVQL
          LRT...L..H...QKW.DKQYKKAHLGTA.LKAN.FG.ASH.K..VLEK..GVEA..PNS.IRKC..VQL
Retrocopy LRT-KNLPVH*QEQKWNDKQYKKAHLGTA<LKANAFGNASHTKRTVLEK<IGVEAEWPNSNIRKCTIVQL

Parental  IKNGKKITAFVPNDGCLNFIEE-NDEVLVAG-FGRKGHAVGDIPGVRFKVVKVANVS
          I.NGKKI..FVPNDGCLNFIEE..DE.LVA...G.KG..V.DIP.VRF.VV.VA.VS
Retrocopy IENGKKIIVFVPNDGCLNFIEE<KDEFLVAE<IGQKGGTVVDIPVVRFNVVRVASVS

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	86.75 RPM
SRP007412_cerebellum	0.00 RPM	89.63 RPM
SRP007412_heart	0.00 RPM	50.59 RPM
SRP007412_kidney	0.00 RPM	265.61 RPM
SRP007412_liver	0.00 RPM	271.35 RPM
SRP007412_testis	0.00 RPM	118.93 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_1316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1316 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3287
Pan troglodytes	retro_ptro_2223
Pongo abelii	retro_pabe_2716

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Homo sapiens	ENSG00000186468	6 retrocopies	retro_hsap_1778, retro_hsap_2940, retro_hsap_3107, retro_hsap_3287, retro_hsap_3989, retro_hsap_4697,
Gorilla gorilla	ENSGGOG00000025014	6 retrocopies	retro_ggor_1316 , retro_ggor_2038, retro_ggor_2131, retro_ggor_2237, retro_ggor_2677, retro_ggor_286,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Monodelphis domestica	ENSMODG00000020255	3 retrocopies	retro_mdom_1518, retro_mdom_1612, retro_mdom_395,
Mustela putorius furo	ENSMPUG00000008114	1 retrocopy	retro_mputfur_1298,
Nomascus leucogenys	ENSNLEG00000013203	3 retrocopies	retro_nleu_1353, retro_nleu_1909, retro_nleu_764,
Oryctolagus cuniculus	ENSOCUG00000010363	2 retrocopies	retro_ocun_195, retro_ocun_95,
Rattus norvegicus	ENSRNOG00000016580	12 retrocopies	retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Sus scrofa	ENSSSCG00000014133	1 retrocopy	retro_sscr_92,