RetrogeneDB ID: retro_cjac_638

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:174803955..174805226(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSCJAG00000000793
• Aliases: None
• Description: splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]

Sequence

>retro_cjac_638
ATGGCTGCCGGGCCGATCTCAGAGCGGAACCAGGATGCCACTGTGTACGTCGGGGGCCTGGATGAGAAGGTTAGTGAACC
GCTGCTGTGGGAACTGTTTCTCCAGGCTGGACCAGTAGTCAACACTCACATGCCAAAGGAGAGAGTCACTGGCCAGCACC
CAGGCTATGGCTTTGTGGAATTCTTGAGTGAGGAAGATGCAGACTATGTCATTAAAATCATGAACATGATCAAACTCTAT
GGGAAGCCAATACGGTGAACAAGGCATCAGCTCACAACAAAAACCTGGATGTAGGAGCCAACATTTTCATTGGCAACCTG
GACCCTGAGATTGATGAGAAGTTGCTTTATGATACTTTCAGCGCCTTTGGGGCCATCTTACAAACCCCTAAGATTATGCA
GGACCCTGACACAGGCAACTCCAAAGGTTATGCCTTTATTAATTTTGCTTCATTTGATGCTTCGGATGCAGCAATTGAAG
CCATGAATGGGCAGTACCTCTGTAACCGCCCTATCACTGTATCTTATGCCTTCAAGAAGGACTCCAAGGGTGAGCGCCAT
GGCTCAGCAGCCGAACGACTTTTGGCAGCTCAGAACCCACTCTCCCAGGCTGACCGCCCTCATCAGCTATTTGCAGATGC
ACCTCCTCCACCCTCTGCCCCCAATCCTGTGGTATCATCACTGGGGTCTGGGCTTCCTCCACCAGGCATGCCTCCTCCTG
GCTCCTTCCCAACCCCAGTGCTGCCTCCTGGAGCCCTCCCACCTGGGATACCCCCAGCCATGCCCCCACCACCTATGCCG
CCTGGGGCTGCAGAACATGGCCCCCCATTGGCAGGAACCCCAGGGGCAGGACATCCTGGTCATGGACACTCACATCCTCA
TCCATTCCCACCAGGTGGGATGCCCCATCCAGGGATGTCTCAGATGCAGCTGGCACACCATGGCCCTCATGGCTTAAGAC
ATCCCCATGCTGGACCCCCAGGCTCTGGGGGGCAGCCACCGCCCTGACCACCACCTGGAATGCCTCATCCTGGACCTCCT
CCAATGGGCATGCCGCCCCGAGGGCCTCCATTTGGATCTCCCATGGGTCACCCAGGTCCTATGCCTCCACATGGTATGCG
TGGACCTCCTCCACTGATGCCCCTCCATGGATACACTGGCCCTCCACGGCCCCCACCCTATGGCTACCAGCGGGGGCCTC
TCCCTCCACCCAGACCCACTTCCCGGCCACCAGTTCTCCCTCAAGGCCCGCTTCGGGGCCCTCTCCCTCAG

Alignment

ORF - retro_cjac_638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
          MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPK.RVTGQH.GYGFVEFLSEEDADY.
Retrocopy MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKERVTGQHPGYGFVEFLSEEDADYV

Parental  IKIMNMIKLYGKPIR-VNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTG
          IKIMNMIKLYGKPIR.VNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFG.ILQTPKIM.DPDTG
Retrocopy IKIMNMIKLYGKPIR<VNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGAILQTPKIMQDPDTG

Parental  NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ
          NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ
Retrocopy NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ

Parental  LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAG
          LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFP.PV.PPGALPPGIPPAMPPPPMPPGAA.HGPP.AG
Retrocopy LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPTPVLPPGALPPGIPPAMPPPPMPPGAAEHGPPLAG

Parental  TPGAGHPGHGHSHPHPFPPGGMPHPGMTQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPM
          TPGAGHPGHGHSHPHPFPPGGMPHPGM.QMQLAHHGPHGL.HPHAGPPGSGGQPPP.PPPGMPHPGPPPM
Retrocopy TPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLRHPHAGPPGSGGQPPP*PPPGMPHPGPPPM

Parental  GMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLR
          GMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMP.HGYTGPPRPPPYGYQRGPLPPPRPT.RPPV.P.GPLR
Retrocopy GMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPLHGYTGPPRPPPYGYQRGPLPPPRPTSRPPVLPQGPLR

Parental  GPLPQ
          GPLPQ
Retrocopy GPLPQ

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
SRP051959_colon	0.00 RPM	3.93 RPM
SRP051959_heart	0.00 RPM	3.07 RPM
SRP051959_kidney	0.00 RPM	4.13 RPM
SRP051959_liver	0.00 RPM	2.49 RPM
SRP051959_lung	0.02 RPM	5.08 RPM
SRP051959_lymph_node	0.02 RPM	5.14 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.51 RPM
SRP051959_spleen	0.00 RPM	3.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_638 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_638 has 0 orthologous retrocopies within eutheria group .

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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,