RetrogeneDB ID: retro_ggor_1056

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:48289470..48290733(+)
• Located in intron of: ENSGGOG00000003117

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSGGOG00000004761
• Aliases: None
• Description: None

Sequence

>retro_ggor_1056
ATGGCTACCAGGCCAATCTCCGAGCGGAACCAGGATGCCACTGTGTACATGGGGGGCCTGAATGAGAAGGTTAGTGAACC
GCTGCTGTGGGAACTGTTTCTCCAGGCTGGACCAGTAGTCAATACCCACATGCCAAAGGATAGAGTCACTGGCCAGCACC
AAGGCTATGACTTTGTGAATTCTTGAGTGAGGATGATGCTGACTATGCCATTAAGATCATGAACATGATCAGACTCTATG
GGAAGCCAATACGGGTGAACAAGGCATCAGCTCACGACAAAAACCTGGATGTAGGGGCCAACATTTTCATTGGGAACCTG
GACCCTGAGATTGATGAGAAGTTGCTTTATGATACTTTCAGCGCCTTTGGGGTCATCTTACAAACCCCCAAGATTATGTG
GGACCCTGACACAGGCAACTCCAAAGGTTATGCCTTTATTAATTTTGCTTCGTTTGATGCTTCAGTTGCAGCAATTGAAG
CCATGAATGGGCAGTATCTCTGTAACCACCCTATCACCGTATCTTATGCCTTCGAGAAGGACTCCAAGGGTGAGCGCCAT
GGATTAGCAGCCGGACGACTTCTGGCAGCTCAGAACCCGTTCTCCCAGCCTGACCGCCCTCATCAGCTGTTTGCAGATGC
ACCTCCTTCACCCTCTGCCCCCAATCCTGTGGTATAATCATTGGGGTCTGGGCTTCCTCCACCAGGCATGCCTCCTCCTG
GCTCCTTCCCACCCCCAGTGCCGCCTCCTGGAGCCCTCCCACCTGGGATACCCCCAGCCATGCCCCACCACCTATGCCTC
CTGAGGCTGCAGGACATGGCCCACCATCGGCAGGAACCCCAGGGGCAGGACATCCTGGTCATGGACACTCCCAAGCTCAC
CCATTCCCACCAGGAGGAGTGCCCCATCCAGGGATGTCTCAGATGCAGCTGGCACACCATGGACCTCATGGTTTAGGACA
TCCCCATTCTGGACACCCAGGCTCTGGGGGACAGCCACCGCCCCAACCACCACCTGGAATGCCTCATCCTGGACCTCCTC
CAATGGGCATGCCCCCCCGAGGGCCTCCATTCTGATCTCCCATGGGTCACCCAGGTCCTATGCCTCCACATGGTATGCGT
GGACTTCCTCCACTGATGCCCCCCATGGATACACTGGCCCTCCACAACCCACACCCTATGGCTACCAGCCTCTCCCTCCA
ACCAGACCCACTCCCCAGCCACCAGTTGCCTCTCGAGGCCTGCTTTGGAGCCCTCTCCCTCAG

Alignment

ORF - retro_ggor_1056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFV-EFLSEEDADY
          MA..PISERNQDATVY.GGL.EKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY.FV.EFLSE.DADY
Retrocopy MATRPISERNQDATVYMGGLNEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYDFV<EFLSEDDADY

Parental  AIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTG
          AIKIMNMI.LYGKPIRVNKASAH.KNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIM.DPDTG
Retrocopy AIKIMNMIRLYGKPIRVNKASAHDKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMWDPDTG

Parental  NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ
          NSKGYAFINFASFDAS.AAIEAMNGQYLCN.PITVSYAF.KDSKGERHG.AA.RLLAAQNP.SQ.DRPHQ
Retrocopy NSKGYAFINFASFDASVAAIEAMNGQYLCNHPITVSYAFEKDSKGERHGLAAGRLLAAQNPFSQPDRPHQ

Parental  LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMP-PPPMPPGAAGHGPPSA
          LFADAPP.PSAPNPVV.SLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMP.PPPMPP.AAGHGPPSA
Retrocopy LFADAPPSPSAPNPVV*SLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMP<PPPMPPEAAGHGPPSA

Parental  GTPGAGHPGHGHSHPHPFPPGGMPHPVGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPP
          GTPGAGHPGHGHS..HPFPPGG.PHP.GMSQMQLAHHGPHGLGHPH.G.PGSGGQPPP.PPPGMPHPGPP
Retrocopy GTPGAGHPGHGHSQAHPFPPGGVPHP-GMSQMQLAHHGPHGLGHPHSGHPGSGGQPPPQPPPGMPHPGPP

Parental  PMGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMP-PHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRG
          PMGMPPRGPPF.SPMGHPGPMPPHGMRG.PPLMP.PHGYTGPP.P.PYGYQ..PLPP.RPTP.PPV..RG
Retrocopy PMGMPPRGPPF*SPMGHPGPMPPHGMRGLPPLMP<PHGYTGPPQPTPYGYQ--PLPPTRPTPQPPVASRG

Parental  PLRGPLPQ
          .L..PLPQ
Retrocopy LLWSPLPQ

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	0.05 RPM	21.05 RPM
SRP007412_cerebellum	0.20 RPM	28.88 RPM
SRP007412_heart	0.00 RPM	10.23 RPM
SRP007412_kidney	0.00 RPM	20.98 RPM
SRP007412_liver	0.00 RPM	14.96 RPM
SRP007412_testis	17.61 RPM	49.94 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1056 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1356
Pan troglodytes	retro_ptro_930
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 ,
Gorilla gorilla	ENSGGOG00000009941	1 retrocopy	retro_ggor_1696,
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,