RetrogeneDB ID: retro_pabe_3403

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:43501561..43502113(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000019200
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSPPYG00000004751
• Aliases: None
• Description: Ras-related protein Rap-1b [Source:UniProtKB/Swiss-Prot;Acc:Q5RDM6]

Sequence

>retro_pabe_3403
ATGCATGAGTATAAGCTAGTCATTCTTGGCCTAGGAGGTGTTGGAAAGTCTGCTTTGAACGTACAATTTGTTCAAGGAAT
TTTTGTTGAAAAATATGTCCTATGATAGAAGATTCTTATAGAAAGCAAGTTGAAGTAGATGCACAACAGTGTATGCTTGC
AATCTTGGATACTGCAGGAATGGAACAATTTATAGCAAGGAGGGATTTGTACATGAGAAATGGACAAGGCTTTGCATTAG
TTTATTCCATCACAGCACAGTCCACATTTAATGATTTGCAAGACTTGAGAGAACAGATTCTTCGAGTTAAAGACACTGAT
GATGTTCCAATGATTCTTGTTGGTAATAAGTATGACTTGGAAGATGAAAGAGTTGTAGGGAAGGAACAAGGTCAAAAATC
TAGCAAGACAATGGAACAACTGTGCATTCTTAGATTCTTCTACAAAATCAAAAATAAATGTTAATGAGATCTTTTATGAC
CTAGTGCGGCAGATTAACAGAAAAACTCCAGTGCCTGGGAAGGCTCACAAAAAGTCATCATGTCAGCTGCTT

Alignment

ORF - retro_pabe_3403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYD-PTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRD
          M.EYKLV.LG.GGVGKSAL.VQFVQGIFVEKY..P.IEDSYRKQVEVDAQQCML.ILDTAG.EQF.A.RD
Retrocopy MHEYKLVILGLGGVGKSALNVQFVQGIFVEKYV<PMIEDSYRKQVEVDAQQCMLAILDTAGMEQFIARRD

Parental  LYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQ-NLARQW
          LYM.NGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNK.DLEDERVVGKEQGQ.NLARQW
Retrocopy LYMRNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKYDLEDERVVGKEQGQ>NLARQW

Parental  NNCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
          NNCAFL.SS.KSKINVNEIFYDLVRQINRKTPVPGKA.KKSSCQLL
Retrocopy NNCAFLDSSTKSKINVNEIFYDLVRQINRKTPVPGKAHKKSSCQLL

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	14.98 RPM
SRP007412_cerebellum	0.00 RPM	22.74 RPM
SRP007412_heart	0.03 RPM	26.01 RPM
SRP007412_kidney	0.07 RPM	43.22 RPM
SRP007412_liver	0.00 RPM	37.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3403 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3403 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4234
Pan troglodytes	retro_ptro_2877
Gorilla gorilla	retro_ggor_2836
Macaca mulatta	retro_mmul_1151
Callithrix jacchus	retro_cjac_607

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus	ENSDNOG00000019724	18 retrocopies	retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Dipodomys ordii	ENSDORG00000001086	1 retrocopy	retro_dord_521,
Erinaceus europaeus	ENSEEUG00000010052	1 retrocopy	retro_eeur_327,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Homo sapiens	ENSG00000127314	2 retrocopies	retro_hsap_3338, retro_hsap_4234,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Microcebus murinus	ENSMICG00000013148	1 retrocopy	retro_mmur_116,
Myotis lucifugus	ENSMLUG00000016606	2 retrocopies	retro_mluc_1126, retro_mluc_2211,
Macaca mulatta	ENSMMUG00000011442	2 retrocopies	retro_mmul_1151, retro_mmul_1863,
Monodelphis domestica	ENSMODG00000007323	5 retrocopies	retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Oryctolagus cuniculus	ENSOCUG00000029552	5 retrocopies	retro_ocun_1132, retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Procavia capensis	ENSPCAG00000010977	1 retrocopy	retro_pcap_8,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pongo abelii	ENSPPYG00000004369	1 retrocopy	retro_pabe_2870,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403 ,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000005197	3 retrocopies	retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tarsius syrichta	ENSTSYG00000000192	1 retrocopy	retro_tsyr_910,
Tursiops truncatus	ENSTTRG00000015712	2 retrocopies	retro_ttru_1105, retro_ttru_134,
Vicugna pacos	ENSVPAG00000000931	2 retrocopies	retro_vpac_283, retro_vpac_408,