RetrogeneDB ID: retro_mmul_2191

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:130301446..130302360(+)
• Located in intron of: ENSMMUG00000029318

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9983
• Ensembl ID: ENSMMUG00000007256
• Aliases: None
• Description: splicing factor 3B subunit 4 [Source:RefSeq peptide;Acc:NP_001248161]

Sequence

>retro_mmul_2191
GATACTTTCAGCACCTTTGGGGTCATCTTACAAACCCCTAAGATTATGTGGGACCCTGACACAGGCAACTCCAAAGCTTA
TGCCTTCATTAATTTTACTTCATTTGATGCTTCGGATGCAGCAATTGAAGCCATGAATGGGCAGTACCTCTGTAACTGCC
CTATCACCATATCTTATGCCTTCAGGAAGGACTCCAAGGGTGAGCGCCATGGCTTAGCAGCTGTACGACTTCTGGCAGCT
CAGAACCTGCTCTCCCAGCCTGACCGCCCTCATCAGCTGTTTGCAGATGCACCTCCTCCACCCTCTGCCCCCAATCCTGT
GGTATTATCATTGGGGTCTGGACTTCCTCCACCAGGCATGCCTCCTCTTGACTCCTTCCCACTCCCAGTGCTGCCTCCTG
GAGCCCTCCCACCTGGGATACCCCCCACCATGCCCTACCACCTATGCCTCCTGGGGCTGCAGGACATGGTCCCCCATCAG
CAGGAACCCCAGAGGCAGGATATCCTGATTATGGACACTCACGAGCTCACCCATTCCCACCAGGAGGGGTGCCCTATCCA
GGGATGTCTCAGATGCAGCTGGCACACCATGGACCTCATGGCTTAGGACATCCCCATTCTGGACACCCAGGCTCTGGGGA
GCAGCCACCACCCCAACCACCACCTGGAATGCCTCATCCTGGACCTCCTCCAATCGGCATGCCCCCCAAGGGTCTCCATT
CGGATCTACCATGGGTCACCCAGGTCCTATGCTTCCACATGGTATGCGTGGACCTCCTCCACTGATGCCCCCCTCATGTG
TACACTGGCCCTGCACGACCCACACCCTATGGCTACCAGCCTCTCCCTCCACCCAGACCCACTCCCCAGCCACCAGTTGC
CCCTTGAGACCTGCTTTGGAGCCCTCTCCCTCAG

Alignment

ORF - retro_mmul_2191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 72.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERH
          DTFS.FGVILQTPKIM.DPDTGNSK.YAFINF.SFDASDAAIEAMNGQYLCN.PIT.SYAF.KDSKGERH
Retrocopy DTFSTFGVILQTPKIMWDPDTGNSKAYAFINFTSFDASDAAIEAMNGQYLCNCPITISYAFRKDSKGERH

Parental  GSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGI
          G.AA.RLLAAQN.LSQ.DRPHQLFADAPPPPSAPNPVV.SLGSGLPPPGMPP..SFP.PV.PPGALPPGI
Retrocopy GLAAVRLLAAQNLLSQPDRPHQLFADAPPPPSAPNPVVLSLGSGLPPPGMPPLDSFPLPVLPPGALPPGI

Parental  PPAMP-PPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGP
          PP.MP..PPMPPGAAGHGPPSAGTP.AG.P..GHS..HPFPPGG.P.PGMSQMQLAHHGPHGLGHPH.G.
Retrocopy PPTMP<LPPMPPGAAGHGPPSAGTPEAGYPDYGHSRAHPFPPGGVPYPGMSQMQLAHHGPHGLGHPHSGH

Parental  PGSGGQPPPRPPPGMPHPGPPPMGMPPR-GPPFGSPMGHPGPMPPHGMRGPPPLM-PPHGYTGPPRPPPY
          PGSG.QPPP.PPPGMPHPGPPP.GMPP..G.PFGS.MGHPGPM.PHGMRGPPPLM.PPH.YTGP.RP.PY
Retrocopy PGSGEQPPPQPPPGMPHPGPPPIGMPPK<GSPFGSTMGHPGPMLPHGMRGPPPLM>PPHVYTGPARPTPY

Parental  GYQRGPLPPPRPTPRPPVPPRGPLRGPLPQ
          GYQ..PLPPPRPTP.PPV.P...L..PLPQ
Retrocopy GYQ--PLPPPRPTPQPPVAP*DLLWSPLPQ

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	0.11 RPM	18.15 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	25.54 RPM
SRP007412_cerebellum	0.06 RPM	16.27 RPM
SRP007412_heart	0.06 RPM	10.25 RPM
SRP007412_kidney	0.12 RPM	18.31 RPM
SRP007412_liver	0.08 RPM	15.48 RPM
SRP007412_testis	0.90 RPM	57.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2191 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2191 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2191 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1356
Pan troglodytes	retro_ptro_930
Gorilla gorilla	retro_ggor_1056

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 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,
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,