RetrogeneDB ID: retro_btau_759

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:35786202..35786694(+)
• Located in intron of: ENSBTAG00000010559

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUSIP1
• Ensembl ID: ENSBTAG00000008072
• Aliases: SFRS13A, FUSIP1
• Description: splicing factor, arginine/serine-rich 13A [Source:RefSeq peptide;Acc:NP_001071594]

Sequence

>retro_btau_759
ATGTCCCGGTACCTGCGCCCCCCCAACACGTCTCTCTTCGTGAGGAACGTGGCTGACGATACCAGGTCTGAAGATTTACG
TCGGGAATTTGGTCGTTATGGTCCTATAGTTGATGTGTATGTTCCACTTGATTTCTACACTCGCCGTCCAAGAGGATTTG
CATATGTTCAATTTGAGGATGTTCGTGATGCTGAAGATGCTTTACATAATTTGGACAGAAAGTGCATTTGTGGACGCCAA
ATTGAAATACAGTTTGCACAGGGGGATCGAAAGACTCCAAATCAGATGAAAGCCAAGGAAGGGAGGAATGTGTATAGTTC
TTCGCGCTATGATGATTATGACAGATACAGACGTTCTAGAAGCCAAAGTTATGACAGAAGAAGATCCAGGAGTCGCTCCT
TCGATTACAACTATAGAAGATCTTATAGTCCTAGAAACAGTAGACCGACTGGAAGACCACGGCGTAGCAGAAGCCATTCC
GACAATGATAGA

Alignment

ORF - retro_btau_759 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.17 %
• Parental protein coverage: 89.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRYLRPPNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN
          MSRYLRPPNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN
Retrocopy MSRYLRPPNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN

Parental  LDRKWICGRQIEIQFAQGDRKTPNQMKAKEGRNVYSSSRYDDYDRYRRSRSRSYDRRRSRSRSFDYNYRR
          LDRK.ICGRQIEIQFAQGDRKTPNQMKAKEGRNVYSSSRYDDYDRYRRSRS.SYDRRRSRSRSFDYNYRR
Retrocopy LDRKCICGRQIEIQFAQGDRKTPNQMKAKEGRNVYSSSRYDDYDRYRRSRSQSYDRRRSRSRSFDYNYRR

Parental  SYSPRN-RPTGRPRRSRSHSDNDR
          SYSPRN.RPTGRPRRSRSHSDNDR
Retrocopy SYSPRNSRPTGRPRRSRSHSDNDR

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	1.08 RPM	88.25 RPM
ERP005899_muscle	1.43 RPM	55.69 RPM
SRP017611_brain	1.92 RPM	30.61 RPM
SRP017611_kidney	2.90 RPM	67.75 RPM
SRP017611_liver	1.81 RPM	35.34 RPM
SRP030211_testis	4.95 RPM	71.76 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_759 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_759 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009869	2 retrocopies	retro_amel_1810, retro_amel_355,
Bos taurus	ENSBTAG00000008072	1 retrocopy	retro_btau_759 ,
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Gorilla gorilla	ENSGGOG00000000392	4 retrocopies	retro_ggor_1044, retro_ggor_1411, retro_ggor_1522, retro_ggor_2870,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Mustela putorius furo	ENSMPUG00000015845	1 retrocopy	retro_mputfur_353,
Nomascus leucogenys	ENSNLEG00000013180	3 retrocopies	retro_nleu_1647, retro_nleu_1825, retro_nleu_202,
Oryctolagus cuniculus	ENSOCUG00000029326	1 retrocopy	retro_ocun_717,
Otolemur garnettii	ENSOGAG00000015374	2 retrocopies	retro_ogar_2650, retro_ogar_2987,
Pongo abelii	ENSPPYG00000001726	4 retrocopies	retro_pabe_1115, retro_pabe_1601, retro_pabe_1796, retro_pabe_2529,
Rattus norvegicus	ENSRNOG00000007992	3 retrocopies	retro_rnor_1657, retro_rnor_2800, retro_rnor_2829,
Ictidomys tridecemlineatus	ENSSTOG00000000956	1 retrocopy	retro_itri_1333,
Tursiops truncatus	ENSTTRG00000016150	2 retrocopies	retro_ttru_1098, retro_ttru_695,