RetrogeneDB ID: retro_pabe_500

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:8503180..8504072(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF38A
• Ensembl ID: ENSPPYG00000001348
• Aliases: None
• Description: pre-mRNA-splicing factor 38A [Source:RefSeq peptide;Acc:NP_001125092]

Sequence

>retro_pabe_500
CCAACCCTCAATATCTGGTGGAGAAGATCATTCGAACGCGAATCTGTGAATCCAAGTACTGGAAAGAGGAGTGCTTTGGA
CTTATGGCTGAACTTGTAGTCGATAAAGCCATGGAGTTAATGTTTGTGGGTGGCGTCTATGGTGGCAACATAAAACAAAC
ACCCTTTCTGTGTTTAATCTTGAAGATGCTTCAGATTCAATCCGAGAAAAGTATCACTGTAGAGTTTATAGAAAATGAAG
ATTTCAAGTATGTCCACATGTTGGGGGCACTTTACATGAGGCTGATGGGCACTGCAATTGATTGCTACAAGTACTTGGAG
CCTTTGTACAATGACTATTGAAAAATCAAGAGCCAGAACCGAAATGGGGGTTTGAACTGATGCATGTAGATGAGTTTATT
GATGAACTAGTGCACAGTGAGAGAGTCTGTGATATCATTCTGCCCCGGCTACAGAAACGCTAGCTATTAGAGGAAGCTGA
ACAACTGGAGCCTTGAGTTAGTGCTCTGGAAGAGGACACGGACGACGTGGAGTCCAGTGAAGAGGAAGAAGAGGAGGATG
AGAAGTTGCAAAGAGTGCCATCACCTGATCACCGCCGGAGAAGCTACGGAGACTTGGACAAGCCCCGTCCCTCTCCCACA
CTGTGCTACAGAAGGAGTAGGAGTCGGTCTCCCAGAAGGCGGAATCGATCTCCCAAAAGGAGAAGCCCCTTCTCCCGCCG
AGAAAGGCATCCGAACAAGAGTCCAAGACATCACCGCAGCAGATCCCGAGATCGGCGGCACAGATCCCGTTCCAAGTCCC
CAGATCCTCCCCGTAGTCACAGACACAGGAGCCACTCAAAGTCTCCCAAAATGTCTAAGAAGAGCCACAAGAAGAGCCGG
AGCGGGAATGAG

Alignment

ORF - retro_pabe_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 95.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PTL-KYLVEKDHSNAKSMSSKYWKEECFGLTAELVVDK-LELRFVGGVYGWAIIKTQHPFLCLTL-MLQI
          PTL..YLVEK.........SKYWKEECFGL.AELVVDK..EL.FVGGVYG..I..T..PFLCL.L.MLQI
Retrocopy PTL<QYLVEKI-IRTRICESKYWKEECFGLMAELVVDKAMELMFVGGVYGGNIKQT--PFLCLILKMLQI

Parental  QPE-DIIVEFIKNEDFKYVRMLGALYMRLTGTAIDCYKYLEPLYNDYRKIKSQNRNGE-FELMHVDEFID
          Q.E..I.VEFI.NEDFKYV.MLGALYMRL.GTAIDCYKYLEPLYNDY.KIKSQNRNG..FELMHVDEFID
Retrocopy QSEKSITVEFIENEDFKYVHMLGALYMRLMGTAIDCYKYLEPLYNDY*KIKSQNRNGG<FELMHVDEFID

Parental  ELLHSERVCDIILPRLQKRYVLEEAEQLEPRVSALEEDMDDVESSEEEEEEDEKLERVPSPDHRRRSYRD
          EL.HSERVCDIILPRLQKR..LEEAEQLEP.VSALEED.DDVESSEEEEEEDEKL.RVPSPDHRRRSY.D
Retrocopy ELVHSERVCDIILPRLQKR*LLEEAEQLEP*VSALEEDTDDVESSEEEEEEDEKLQRVPSPDHRRRSYGD

Parental  LDKPRRSPTLRYRRSRSRSPRRRSRSPKRRSPSPRRERHRSKSPRRHRSRSRDRRHRSRSKSPGHHRSHR
          LDKPR.SPTL.YRRS..............RSP..RRERH..KSPR.HRSRSRDRRHRSRSKSP...RSHR
Retrocopy LDKPRPSPTLCYRRSXXXXXXXXXXXXXXRSPFSRRERHPNKSPRHHRSRSRDRRHRSRSKSPDPPRSHR

Parental  HRSHSKSPERSKKSHKKSRRGNE
          HRSHSKSP..SKKSHKKSR.GNE
Retrocopy HRSHSKSPKMSKKSHKKSRSGNE

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	0.83 RPM	28.03 RPM
SRP007412_cerebellum	2.07 RPM	70.04 RPM
SRP007412_heart	0.96 RPM	17.55 RPM
SRP007412_kidney	1.16 RPM	30.13 RPM
SRP007412_liver	1.16 RPM	23.29 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_500 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_500 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_541
Pan troglodytes	retro_ptro_406
Gorilla gorilla	retro_ggor_494

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227, retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500 , retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406, retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13, retro_tgut_14,