RetrogeneDB ID: retro_pabe_2703

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:162620328..162620661(+)
• Located in intron of: ENSPPYG00000016005

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRB
• Ensembl ID: ENSPPYG00000018763
• Aliases: None
• Description: Cytochrome b-c1 complex subunit 7 [Source:UniProtKB/Swiss-Prot;Acc:Q5RC24]

Sequence

>retro_pabe_2703
ATGGCTGGCAAGAAGGCTGTTGCAGCATCAGGCAAGTGGCTGGATGGTATTCAAAAATGGTATTACAATGCCGCAGGATT
CAATAAACTGGGGTTAATGAGAGATGATACAACATATGAGAATGAAGATGTAAAAGAAGCCATAAGAAGACTTTCTGAGA
ACCTTTATAATGACAGGATGTTTCACATGAAGAGGGCACTGGATCTGTCCATGAAGCATCAGATCTTGCCTAAAGAGCAG
CGGACCAAATACGAAGAGGAAAATTTCTACCTTGAACCGTATCTGAAAGAGGTTATTCGGGAATGAAAAGAAAGAGAAGA
ATGGGCAAAGAGG

Alignment

ORF - retro_pabe_2703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGKQAVSASGKWLDGIRKWYYNAAGFNKLGLMRDDTIYEDEDVKEAIRRLPENLYNDRMFRIKRALDLS
          MAGK.AV.ASGKWLDGI.KWYYNAAGFNKLGLMRDDT.YE.EDVKEAIRRL.ENLYNDRMF..KRALDLS
Retrocopy MAGKKAVAASGKWLDGIQKWYYNAAGFNKLGLMRDDTTYENEDVKEAIRRLSENLYNDRMFHMKRALDLS

Parental  LKHQILPKEQWTKYEEENFYLEPYLKEVIRERKEREEWAKK
          .KHQILPKEQ.TKYEEENFYLEPYLKEVIRE.KEREEWAK.
Retrocopy MKHQILPKEQRTKYEEENFYLEPYLKEVIRE*KEREEWAKR

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	41.63 RPM
SRP007412_cerebellum	0.24 RPM	40.25 RPM
SRP007412_heart	0.09 RPM	265.63 RPM
SRP007412_kidney	0.07 RPM	67.65 RPM
SRP007412_liver	0.00 RPM	51.87 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2703 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2703 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2703 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3261
Macaca mulatta	retro_mmul_2053

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007287	1 retrocopy	retro_amel_985,
Canis familiaris	ENSCAFG00000009449	4 retrocopies	retro_cfam_1504, retro_cfam_1509, retro_cfam_1531, retro_cfam_792,
Callithrix jacchus	ENSCJAG00000020560	2 retrocopies	retro_cjac_2206, retro_cjac_894,
Cavia porcellus	ENSCPOG00000012149	2 retrocopies	retro_cpor_1086, retro_cpor_866,
Erinaceus europaeus	ENSEEUG00000001312	1 retrocopy	retro_eeur_224,
Felis catus	ENSFCAG00000026302	5 retrocopies	retro_fcat_1292, retro_fcat_178, retro_fcat_1780, retro_fcat_378, retro_fcat_558,
Homo sapiens	ENSG00000156467	2 retrocopies	retro_hsap_3261, retro_hsap_4838,
Gorilla gorilla	ENSGGOG00000026528	1 retrocopy	retro_ggor_3017,
Latimeria chalumnae	ENSLACG00000004465	1 retrocopy	retro_lcha_127,
Loxodonta africana	ENSLAFG00000002542	1 retrocopy	retro_lafr_727,
Myotis lucifugus	ENSMLUG00000007182	1 retrocopy	retro_mluc_1601,
Macaca mulatta	ENSMMUG00000008804	3 retrocopies	retro_mmul_2053, retro_mmul_2065, retro_mmul_2581,
Mus musculus	ENSMUSG00000021520	4 retrocopies	retro_mmus_1175, retro_mmus_1628, retro_mmus_2610, retro_mmus_514,
Nomascus leucogenys	ENSNLEG00000026670	1 retrocopy	retro_nleu_1357,
Oryctolagus cuniculus	ENSOCUG00000008113	3 retrocopies	retro_ocun_1149, retro_ocun_345, retro_ocun_570,
Otolemur garnettii	ENSOGAG00000004302	1 retrocopy	retro_ogar_1451,
Ochotona princeps	ENSOPRG00000008892	2 retrocopies	retro_opri_109, retro_opri_688,
Pongo abelii	ENSPPYG00000018763	2 retrocopies	retro_pabe_2703 , retro_pabe_3762,
Rattus norvegicus	ENSRNOG00000024967	1 retrocopy	retro_rnor_290,
Sorex araneus	ENSSARG00000002999	3 retrocopies	retro_sara_460, retro_sara_52, retro_sara_704,
Ictidomys tridecemlineatus	ENSSTOG00000008017	1 retrocopy	retro_itri_46,
Tarsius syrichta	ENSTSYG00000010502	2 retrocopies	retro_tsyr_1114, retro_tsyr_898,
Drosophila melanogaster	FBgn0030733	1 retrocopy	retro_dmel_22,