RetrogeneDB ID: retro_btau_1387

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:68253262..68254201(+)
• Located in intron of: ENSBTAG00000013912

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE4A
• Ensembl ID: ENSBTAG00000019166
• Aliases: None
• Description: Non-structural maintenance of chromosomes element 4 homolog A [Source:UniProtKB/Swiss-Prot;Acc:Q2TBI1]

Sequence

>retro_btau_1387
GGGAAGGCCGACATCGACCCCAGCCTGCTGGAGCGTGTGGATGAAGAGAAATGTCGGAGTATCCGCAAGCAGTACCGGCA
GCTCATCTATACCGTCCAGCAGAACCGTGACGACATAGTGAACACGGCGAGCGACTCCTTAACCGAGGCTCTCGAGGAAG
CCAATGTCCTGTTTGATGCAGTGAGTCGAACAAGAGAAGCGGCTCTCGACTCTCAGTTTCTTGTTTTGGCTTCTGATTTG
GGTAAAGAAAAAGCAAAGCACCTGAACTCTGACATGAACTTTTTTAATCAGGTGGCATTCTGTGACTTTCTGTTTATATT
TGTGGGTCTAAATTGGATGGAAGATGACGAACGTGATCCGTTGAATAACTGTGACGATAACATAGCTCTTTCCTTCTGGG
AGACAGTACAGAAGGAAGCGACATCGTGTATATCACAAGCTGAAACATTCCACTTTCTTTTTGGTTCGTTCAAACCAGAG
TCTGCTGCGCGAAAGCCGCGACGTAATCACCGGAGAAAAGTGCAGAAAATGGAAGAGAATGGGGTTATGCCTACAAAGCT
GAGGAAGCTGGATCTGAGTGGTAATCAAGAAGCCACAGAAAAAGAAGTAGAAAGAATTTTGGGATTGTTGCAAACGTACT
TTCGAAAGTATCCTGATACTCCTGTGTCTTATTTTGAGTTTGTGATTGATCCAAACTCTTTCTCTCGTACTGTGGAGAAT
ATATTTTATGTTTCTTTCATTATAAGGGATGGTTTTGCAAGAATAAGGCTTGACCAAGACAGGCTGCCAATATTAGAGCC
AATTAATATTAACCTAGCCGGTGAGGGAAATGATCCCAGTTTCCACAGCAGGAAACAGGGAGTTATATCTTTGAGTTTAC
AAGACTGGAAAAATATTGTGGCAGCTTTCGAAATTTCAGAGGCTATGATCACAAACTCG

Alignment

ORF - retro_btau_1387 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.01 %
• Parental protein coverage: 81.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDEMIDPASLEEETDPSLCRQIRHQYRALINSVQQNREDILN-ASDKLTEVLEEANTLFNGVSRAREAVL
          G...IDP.SL.E..D...CR.IR.QYR.LI..VQQNR.DI.N.ASD.LTE.LEEAN.LF..VSR.REA.L
Retrocopy GKADIDP-SLLERVDEEKCRSIRKQYRQLIYTVQQNRDDIVNTASDSLTEALEEANVLFDAVSRTREAAL

Parental  DAHFLVLASDLGKEKAKQLRSDLNSFDMLRYVETLLTHMGVNPLEAEELIRDEDSSDLEFIVYDSWKISG
          D..FLVLASDLGKEKAK.L.SD.N.F........L....G.N..E..E..RD........I....W....
Retrocopy DSQFLVLASDLGKEKAKHLNSDMNFFNQVAFCDFLFIFVGLNWMEDDE--RDPLNNCDDNIALSFWETVQ

Parental  KTAENTFNKTHTFHFLLGSIQGECPVPKPRIERPRKVRMIEEQQAMPAQLKRMEES-HQEATEKEVERIL
          K.A........TFHFL.GS...E....KPR....RKV...EE...MP..L.....S..QEATEKEVERIL
Retrocopy KEATSCISQAETFHFLFGSFKPESAARKPRRNHRRKVQKMEENGVMPTKLRKLDLSGNQEATEKEVERIL

Parental  GLLQTYFQEDPDTPMSFFDFVVDPHSFPRTVENIFHVSFIIRDGFARIRLDRDRLPVIEPVNINEESGGN
          GLLQTYF...PDTP.S.F.FV.DP.SF.RTVENIF.VSFIIRDGFARIRLD.DRLP..EP.NIN....GN
Retrocopy GLLQTYFRKYPDTPVSYFEFVIDPNSFSRTVENIFYVSFIIRDGFARIRLDQDRLPILEPININLAGEGN

Parental  T---QIRNQAIIALSYRDWEEIVRTFEISEPVITSS
          ......R.Q..I.LS..DW..IV..FEISE..IT.S
Retrocopy DPSFHSRKQGVISLSLQDWKNIVAAFEISEAMITNS

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	6.63 RPM	33.67 RPM
ERP005899_muscle	0.90 RPM	18.42 RPM
SRP017611_brain	8.09 RPM	9.55 RPM
SRP017611_kidney	7.47 RPM	29.04 RPM
SRP017611_liver	2.19 RPM	8.53 RPM
SRP030211_testis	69.89 RPM	11.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_btau_1387 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AJ694856	68253193	68253547	99.5	352	1	349
DY158011	68253214	68253582	99.2	365	3	362

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1387 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_43
Macaca mulatta	retro_mmul_716
Canis familiaris	retro_cfam_379
Equus caballus	retro_ecab_109

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387 ,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,