RetrogeneDB ID: retro_btau_592

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:27883640..27884385(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000039673
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSBTAG00000012495
• Aliases: None
• Description: splicing factor 3B subunit 4 [Source:RefSeq peptide;Acc:NP_001192513]

Sequence

>retro_btau_592
CAGAAGGACTCCAAGGGCGAGTGCCATGGCTCAGCAGCTGAACGACTTGTGGCAGCACAGAACCACTCTCCCAGGCTGAC
GACCCTCATCAGCTGTTTGCCGATGCACCATCTCCACCCTCTGCGTCCAATCCTGTGGTATCATCTTTGAGGTCTGGGCT
TCCTCCTCCATGCATGCCTCCTTCTGGCTCTGTCCCACCCCCAGTACTGCCTCCTGGAGCCCTTCCACTCAGGATATCCG
CAGTCATGCCCCCCCACCTATGCCTCCTGGGGCTGGAGGACATGGTCCCCCATCAGCGGGAACCCCAGGGGCTGGACATC
CTGGACACGGACACTCACATCCTCACCCATTCCCACTGGGTGGGATGCTCCATCTAGAGATGTCTCAGATGCAGCTGGTC
CACCATAGCCCTCACGGCTTGGGACAGCCCCATGCTGGGCCCCCTGGCTCTGGAGGGCAGCCATCACCCCAACCACCACC
TGGGATGCGTCACCCTTGACATCTTCTCATGAGCATGCCCCACCCCCACCAGGGGCCTCTGTTTGGCTCTACTGTGGGTC
TCCCAGTCCTATGCCTCCGCATGGTATGCATGGACCTCCTCTACTGATGCCCCCTAACGGATGGATACACTGGCCCTCCA
TGACCTCCACCCTATGGCTACCAGTGGGGGCCGTTCCCTCCACCCAGACCCACTTCCTGGTCTCCAGTTCCCCCTCGAGG
CCCACTTCGAGGCCTTCTCCCTCGG

Alignment

ORF - retro_btau_592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.89 %
• Parental protein coverage: 58.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKDSKGERHGSAAERLLAAQN-PLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPV
          .KDSKGE.HGSAAERL.AAQN.PLSQAD.PHQLFADAP.PPSA.NPVVSSL.SGLPPP.MPP.GS.PPPV
Retrocopy QKDSKGECHGSAAERLVAAQN<PLSQADDPHQLFADAPSPPSASNPVVSSLRSGLPPPCMPPSGSVPPPV

Parental  PPPGALPPGIPPAMP-PPPMPPGAGGHGPPSAGTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGP
          .PPGALP..I...MP.PPPMPPGAGGHGPPSAGTPGAGHPGHGHSHPHPFP.GGM.H..MSQMQL.HH.P
Retrocopy LPPGALPLRISAVMP<PPPMPPGAGGHGPPSAGTPGAGHPGHGHSHPHPFPLGGMLHLEMSQMQLVHHSP

Parental  HGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGM--PPRGPPFGSPM-GHPGPMPPHGMRGPPPLMPPH
          HGLG.PHAGPPGSGGQP.P.PPPGM.HP....M.M..P..GP.FGS...G.P.PMPPHGM.GPP.LMPP.
Retrocopy HGLGQPHAGPPGSGGQPSPQPPPGMRHP*HLLMSMPHPHQGPLFGSTV<GSPSPMPPHGMHGPPLLMPPN

Parental  GYTGPPRP-PP-YGYQRGPLPPPRPTPRPPVPPRGPLRGPLPQ
          G....P...PP.YGYQ.GP.PPPRPT...PVPPRGPLRG.LP.
Retrocopy GWIHWPSM>PPPYGYQWGPFPPPRPTSWSPVPPRGPLRGLLPR

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
ERP005899_liver	1.15 RPM	8.44 RPM
ERP005899_muscle	0.05 RPM	22.75 RPM
SRP017611_brain	0.00 RPM	24.48 RPM
SRP017611_kidney	0.00 RPM	30.58 RPM
SRP017611_liver	0.23 RPM	12.31 RPM
SRP030211_testis	0.00 RPM	85.73 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_592 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_592 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_592 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 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,
Felis catus	ENSFCAG00000010106	1 retrocopy	retro_fcat_1607,
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,
Mus musculus	ENSMUSG00000068856	1 retrocopy	retro_mmus_1406,
Oryctolagus cuniculus	ENSOCUG00000004614	1 retrocopy	retro_ocun_1239,
Otolemur garnettii	ENSOGAG00000006265	3 retrocopies	retro_ogar_2227, retro_ogar_2388, retro_ogar_2804,
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,