RetrogeneDB ID: retro_pabe_1124

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:68156218..68156781(+)
• Located in intron of: ENSPPYG00000005918

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSPPYG00000000912
• Aliases: None
• Description: splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]

Sequence

>retro_pabe_1124
GGCATGCTTCCTCCTGGCTCCTTCGCACCCCCAGTGCCACCTCCTGGAGCCCTCCCACATGGGATACCCCCAGCCATGCC
CCACCACCTATGCCTCCTGGGGCTGCAGGACATGACCCTCCATCGGCAGGAACCCCAGGGGCAGGACATCCTGGTCATGG
ACACTCACAGGCTCACCCATTCCCACCAGGAGGAGTGCCCCATCCAGGGATGTCTCAGATGCAGCTGGCACACCATGGAC
CTCATGGCTTAGGACATCCCCATTCTGGACCCCCAGGCTCTGGGGGGCAGCCACCACCTCAACCACCACCTGGAATGCCT
CATCCTGGACCTCCTCCAATGGGCATGCCCCCTCCAAGGGCCTCCATTCAGATCTCCCATGGGTCATCCAGGTCCTATGC
CTCCACATGGTATGTGTGGACCTCCTCCACTGATGCCCCCCTCCATGGATACACTGGCCCTCCACGACCCACACCCTGTG
GCTACCAGCCTCTGCCTCCACCCAGACCCACTCCCCAGCCACCAGTTGCCCCTCGAGGCCCGCTTTGGAGCCCTCTCCCT
CAG

Alignment

ORF - retro_pabe_1124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.56 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GMPPPGSFPPPVPPPGALPPGIPPAMP-PPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGGMPHP
          GM.PPGSF.PPVPPPGALP.GIPPAMP.PPPMPPGAAGH.PPSAGTPGAGHPGHGHS..HPFPPGG.PHP
Retrocopy GMLPPGSFAPPVPPPGALPHGIPPAMP<PPPMPPGAAGHDPPSAGTPGAGHPGHGHSQAHPFPPGGVPHP

Parental  GMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPP-RGPPFGSPMGHPGPMPPHGM
          GMSQMQLAHHGPHGLGHPH.GPPGSGGQPPP.PPPGMPHPGPPPMGMPP..GPPF.SPMGHPGPMPPHGM
Retrocopy GMSQMQLAHHGPHGLGHPHSGPPGSGGQPPPQPPPGMPHPGPPPMGMPP>QGPPFRSPMGHPGPMPPHGM

Parental  RGPPPLM-PP-HGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLRGPLPQ
          .GPPPLM.PP.HGYTGPPRP.P.GYQ..PLPPPRPTP.PPV.PRGPL..PLPQ
Retrocopy CGPPPLM>PP>HGYTGPPRPTPCGYQ--PLPPPRPTPQPPVAPRGPLWSPLPQ

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	0.88 RPM	17.20 RPM
SRP007412_cerebellum	0.61 RPM	4.01 RPM
SRP007412_heart	0.36 RPM	2.92 RPM
SRP007412_kidney	0.53 RPM	14.72 RPM
SRP007412_liver	0.24 RPM	5.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1124 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1124 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012495	2 retrocopies	retro_btau_1385, retro_btau_592,
Canis familiaris	ENSCAFG00000011617	3 retrocopies	retro_cfam_585, retro_cfam_711, retro_cfam_729,
Callithrix jacchus	ENSCJAG00000000793	3 retrocopies	retro_cjac_1297, retro_cjac_1909, retro_cjac_638,
Cavia porcellus	ENSCPOG00000008267	1 retrocopy	retro_cpor_234,
Echinops telfairi	ENSETEG00000008963	1 retrocopy	retro_etel_1310,
Homo sapiens	ENSG00000143368	1 retrocopy	retro_hsap_1356,
Gorilla gorilla	ENSGGOG00000004761	1 retrocopy	retro_ggor_1056,
Macaca mulatta	ENSMMUG00000007256	1 retrocopy	retro_mmul_2191,
Mustela putorius furo	ENSMPUG00000005563	2 retrocopies	retro_mputfur_1105, retro_mputfur_648,
Oryctolagus cuniculus	ENSOCUG00000004614	1 retrocopy	retro_ocun_1239,
Pongo abelii	ENSPPYG00000000912	1 retrocopy	retro_pabe_1124 ,
Pongo abelii	ENSPPYG00000003894	1 retrocopy	retro_pabe_1669,
Pan troglodytes	ENSPTRG00000001243	1 retrocopy	retro_ptro_930,
Pteropus vampyrus	ENSPVAG00000014171	1 retrocopy	retro_pvam_931,
Rattus norvegicus	ENSRNOG00000021181	1 retrocopy	retro_rnor_2350,
Ictidomys tridecemlineatus	ENSSTOG00000000684	2 retrocopies	retro_itri_1153, retro_itri_487,