RetrogeneDB ID: retro_ptro_930

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:66331314..66332577(+)
• Located in intron of: ENSPTRG00000006459

Retrocopy information

• Ensembl ID: ENSPTRG00000041203
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSPTRG00000001243
• Aliases: None
• Description: None

Sequence

>retro_ptro_930
ATGGCTACCAGACCGATCTCCGAGCGGAACCAGGATGCCACTGTGTACGTGGGGGGCCTGAATGAGAAGGTTAGTGAACC
GCTGCTGTGGGAACTGTTTCTCCAGGCTGGACCAGTAGTCAACACCCACATGCCAAAGGATAGAGTCACTGGCCAGCACC
AAGGCTATGACTTTGTGAATTCTTGAGTGAGGATGATGCTGACTATGCCGTTAAGATCATGAACATGATCAGACTCTATG
GGAAGCCAATACGGGTGAACAAGGCATCAGCTCACAACAAAAACCTGGATGTAGGGGCCAACATTTTCAATGGGAACCTG
GACCCTGAGATTGATGAGAAGTTGCTTTATGATACTTTCAGCGCCTTTGGGGTCATCTTACAAACCCCCAAGATTATGTG
GGACCCTGACACAGGCAACTCCAAAGGTTATGCCTTTATTAATTTTGTTTCATTTGATGCTTCAGTTGCAGCAATTGAAG
CCATGAATGGGCAGTACCTCTGTAACCACCCTATCACCGTATCTTATGCCTTCGAGAAGGACTCCAAGGGTGAGCGCCAT
GGCTTAGCAGCCGGACGACTTCTGGCAGCTCAGAACCCACTCTCCCAGCCTGACCGCCCTCATCAGCTGTTTGCAGATGC
ACCTCCTTCACCCTCTGCCCCCAATCCTGTGGTATCATCATTGGGGTCTGGGCTTCCTCCACCAGGCATGCCTCCTCCTG
GCTCCTTCCCACCCCCAGTGCTGCCTCCTGGAGCCCTCCCACCTGGGATACCCCCAGCCATGCCCCACCACCTATGCCTC
CTGGGGCTGCAGGACATGGCCCCCCATCGGCAGGAACCCCAGGGGCAGGACATCCTGGTCATGGACACTCCCAAGCTCAC
CCATTCCCACCAGGAGGAGTGCCCCATCCAGGGATGTCTCAGATGCAGCTGGCACACCATGGACCTCATGGTTTAGGACA
TCCCCATTCTGGACACCCAGGCTCTGGGGGACAGCCACCACCCCAACCACCACCTGGAATGCCTTATCCTGGACCTCCTC
CAATGGGCATGCCCCCCCGAGAGCCTCCATTCTGATCTCCCATGGGTCACCCAGGTCCTATGCCTCCACATGGTATGCGT
GGACTTCCTCCACTGATGCCCCCCATGGATACACTGGCCCTCCACAACCCACACCCTATGGCTACCAGCCTCTCCCTCCA
ACCAGGCCCACTCCCCAGCCACCAGTTGCCCCTCGAGGCCCGCTTTGGAGCCCTCTCCCTCAG

Alignment

ORF - retro_ptro_930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFV-EFLSEEDADY
          MA..PISERNQDATVYVGGL.EKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY.FV.EFLSE.DADY
Retrocopy MATRPISERNQDATVYVGGLNEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYDFV<EFLSEDDADY

Parental  AIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTG
          A.KIMNMI.LYGKPIRVNKASAHNKNLDVGANIF.GNLDPEIDEKLLYDTFSAFGVILQTPKIM.DPDTG
Retrocopy AVKIMNMIRLYGKPIRVNKASAHNKNLDVGANIFNGNLDPEIDEKLLYDTFSAFGVILQTPKIMWDPDTG

Parental  NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ
          NSKGYAFINF.SFDAS.AAIEAMNGQYLCN.PITVSYAF.KDSKGERHG.AA.RLLAAQNPLSQ.DRPHQ
Retrocopy NSKGYAFINFVSFDASVAAIEAMNGQYLCNHPITVSYAFEKDSKGERHGLAAGRLLAAQNPLSQPDRPHQ

Parental  LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMP-PPPMPPGAAGHGPPSA
          LFADAPP.PSAPNPVVSSLGSGLPPPGMPPPGSFPPPV.PPGALPPGIPPAMP.PPPMPPGAAGHGPPSA
Retrocopy LFADAPPSPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVLPPGALPPGIPPAMP<PPPMPPGAAGHGPPSA

Parental  GTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPP
          GTPGAGHPGHGHS..HPFPPGG.PHPGMSQMQLAHHGPHGLGHPH.G.PGSGGQPPP.PPPGMP.PGPPP
Retrocopy GTPGAGHPGHGHSQAHPFPPGGVPHPGMSQMQLAHHGPHGLGHPHSGHPGSGGQPPPQPPPGMPYPGPPP

Parental  MGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMP-PHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGP
          MGMPPR.PPF.SPMGHPGPMPPHGMRG.PPLMP.PHGYTGPP.P.PYGYQ..PLPP.RPTP.PPV.PRGP
Retrocopy MGMPPREPPF*SPMGHPGPMPPHGMRGLPPLMP<PHGYTGPPQPTPYGYQ--PLPPTRPTPQPPVAPRGP

Parental  LRGPLPQ
          L..PLPQ
Retrocopy LWSPLPQ

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	0.09 RPM	18.75 RPM
SRP007412_cerebellum	0.07 RPM	24.66 RPM
SRP007412_heart	0.03 RPM	7.32 RPM
SRP007412_kidney	0.10 RPM	31.77 RPM
SRP007412_liver	0.03 RPM	24.16 RPM
SRP007412_testis	9.38 RPM	54.90 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_930 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_930 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_930 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1356
Gorilla gorilla	retro_ggor_1056
Macaca mulatta	retro_mmul_2191

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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,
Pan troglodytes	ENSPTRG00000001243	1 retrocopy	retro_ptro_930 ,
Pan troglodytes	ENSPTRG00000004305	1 retrocopy	retro_ptro_1617,
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,