RetrogeneDB ID: retro_pabe_2761

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:94335079..94335685(-)
• Located in intron of: ENSPPYG00000015631

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000017210
• Aliases: None
• Description: None

Sequence

>retro_pabe_2761
GAGGACACCTCGGGCATACTGAAAGAGTTGCAGCAATTGGCCAAGGAGCTGAGGCGGAAGAGGTTGAGCCTAGGGTACTC
GCAGGCCGATGTGGGGATCGCTGTGGGAGCTCTGTTTGGGAAGGTGCTTAGCCAGACGACCATCTGCCGCTTCGAGGCCC
AGCAGCTAAGCCTCGCCAACATGTGGAAGCTGCGACCACTGCTGAAAAAGTGGCTGGAGGAAGTGGAAGCAGAGAACCTT
CTGGGCTTATGCAAAATGGAGATGATCCTGCAACAGTCTCAGAAGTGGAGACGGGCAAGCAGGGAGCGACGAATCGGAAA
CAGCCTGGAGAAATTCTTCCAGCGGTGCCCTAAGCCCACACCCCAGCAAATCAGCCACATTGCTGGGTGCCTTCAGCTGC
AGAAAGATGTGGTTCGAGTTTGGTTCTATAACCGCAGCAAGATGGGCAGTCGACCAACCAATGATGCTTCCCCACGGGAG
ATTGTGGGGACAGCCGGGCCTCCTTGCCCAGGGGCACCAGTGTGCTTTCACCTGGGACTGGGGCTCCCAGTGGATATCCC
CCACTATACACGTCTCTACTCTGCAGGGGTAGCCCACTCTGCCCCA

Alignment

ORF - retro_pabe_2761 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.22 %
• Parental protein coverage: 56.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQK
          .D.....KEL.Q.AK.L..KR..LGY.QADVG...G.LFGKV.SQTTICRFEA.QLS..NM.KLRPLL.K
Retrocopy EDTSGILKELQQLAKELRRKRLSLGYSQADVGIAVGALFGKVLSQTTICRFEAQQLSLANMWKLRPLLKK

Parental  WVEEADNNENLQEICKAETLV-QARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVR
          W.EE....ENL...CK.E....Q..K..R.S.E.R....LE..F..CPKPT.QQISHIA..L.L.KDVVR
Retrocopy WLEEVE-AENLLGLCKMEMILQQSQKWRRASRERRIGNSLEKFFQRCPKPTPQQISHIAGCLQLQKDVVR

Parental  VWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPHFTALYSSVP
          VWF.NR...G.R...D...RE....AG.P..G.PV.F.L..G.....P.Y..........S.P
Retrocopy VWFYNRSKMGSRPTNDASPREIVGTAGPPCPGAPVCFHLGLGLPVDIPHYTRLYSAGVAHSAP

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	0.06 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.12 RPM
SRP007412_heart	0.06 RPM	0.12 RPM
SRP007412_kidney	0.07 RPM	0.36 RPM
SRP007412_liver	0.03 RPM	0.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2761 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2761 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010377	3 retrocopies	retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus	ENSBTAG00000021111	2 retrocopies	retro_btau_1576, retro_btau_951,
Canis familiaris	ENSCAFG00000000485	1 retrocopy	retro_cfam_1538,
Callithrix jacchus	ENSCJAG00000019789	1 retrocopy	retro_cjac_123,
Dipodomys ordii	ENSDORG00000009549	1 retrocopy	retro_dord_65,
Equus caballus	ENSECAG00000008967	1 retrocopy	retro_ecab_301,
Erinaceus europaeus	ENSEEUG00000015357	2 retrocopies	retro_eeur_196, retro_eeur_558,
Felis catus	ENSFCAG00000001078	3 retrocopies	retro_fcat_1372, retro_fcat_1422, retro_fcat_275,
Gorilla gorilla	ENSGGOG00000027662	3 retrocopies	retro_ggor_2275, retro_ggor_295, retro_ggor_852,
Macropus eugenii	ENSMEUG00000013221	3 retrocopies	retro_meug_1146, retro_meug_1475, retro_meug_692,
Microcebus murinus	ENSMICG00000001511	1 retrocopy	retro_mmur_1423,
Myotis lucifugus	ENSMLUG00000011028	3 retrocopies	retro_mluc_1465, retro_mluc_2382, retro_mluc_515,
Mustela putorius furo	ENSMPUG00000001202	2 retrocopies	retro_mputfur_253, retro_mputfur_96,
Mus musculus	ENSMUSG00000024406	2 retrocopies	retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus	ENSOCUG00000017160	3 retrocopies	retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Otolemur garnettii	ENSOGAG00000000621	3 retrocopies	retro_ogar_1406, retro_ogar_1436, retro_ogar_2229,
Ochotona princeps	ENSOPRG00000003926	2 retrocopies	retro_opri_1213, retro_opri_556,
Pongo abelii	ENSPPYG00000017210	3 retrocopies	retro_pabe_2761 , retro_pabe_3294, retro_pabe_898,
Pan troglodytes	ENSPTRG00000017953	5 retrocopies	retro_ptro_1798, retro_ptro_204, retro_ptro_2132, retro_ptro_2721, retro_ptro_733,
Pteropus vampyrus	ENSPVAG00000007334	2 retrocopies	retro_pvam_724, retro_pvam_74,
Rattus norvegicus	ENSRNOG00000046487	4 retrocopies	retro_rnor_1474, retro_rnor_2186, retro_rnor_2968, retro_rnor_921,
Sus scrofa	ENSSSCG00000001393	2 retrocopies	retro_sscr_252, retro_sscr_678,
Ictidomys tridecemlineatus	ENSSTOG00000026103	3 retrocopies	retro_itri_1076, retro_itri_1705, retro_itri_951,
Tupaia belangeri	ENSTBEG00000013044	4 retrocopies	retro_tbel_3628, retro_tbel_3718, retro_tbel_3779, retro_tbel_4614,
Tarsius syrichta	ENSTSYG00000007340	4 retrocopies	retro_tsyr_1508, retro_tsyr_1630, retro_tsyr_814, retro_tsyr_817,