RetrogeneDB ID: retro_btau_1342

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:33461570..33462441(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.101639
• Ensembl ID: ENSBTAG00000014102
• Aliases: WDR77, MEP50
• Description: methylosome protein 50 [Source:RefSeq peptide;Acc:NP_001015584]

Sequence

>retro_btau_1342
ATGCAGAAGGAAACCCCATCCTTCCTCGTGCCCACACCCTGTGGCCAAAAGTGGAACCCTCCCCCTAACACGCCTGCCTA
TGTAGCAGGTATTGGAGGCTGCACTGTACCTGTTTGATGGGATGTTCCTGCTCCAGGCTTCTAACCTGAGTGACCACTGC
TGGGCTGGCCCCCTCAGGCTTTTCAAGGCCGCTTTGTGCCGCCCCCAAGGAAGGTTTCTGCTTCGCTGGAGTCCAGACAG
AGGCGAGTGGCTAACCTCACTTGGATAGGAGACAGAGGTATCGTAGTGGCTTCTGATCCAGGTGCTGTTGAATTGTGGGA
GCTGGATGAGAATGAGACACTCATTGACAACAAGTTCTGCAAATATAAGCACAATGACATTGTGTCTACAGTCAGTGTCC
TGAGCTCTGGCACACAAGCTGTGAGCTGGTAGCAAAGACTTCTGGATCAAGGTTTGAGACCTTGCTCGGCAGATGGTTCA
AAATTCCTACCGAGCTCATTCTGGGCAGGCCACCTGTGTTGCTGCCTTTCTCCACAAGGATCCTGTGTTTCTTTCATGTG
GCGAGGACAATAGAATCGTATTGGAGGATATCTGCTGTCCCAAGCCAGCCTCACAGATGGGCCATGGTGCCTCTGGCTAC
CTTCTTGCCTCCCTGGCTTTGCATCCTCAGCAGACTGAAGTCTTTGTCTTTGGTGATGAGAATGGGACTGTCCCCCCTGT
GGACACCAAGAGTGCAAGCTGTGCCCTCAGCTCGGTGGTGCAGTCCTAGTGCATCTCTGGGCCGGTGTTCTCTCCACACA
GTGCTCCCTTCCTGGCCTCTGTCAGCCACAACTACTCACTTGCTGTACTGGACTTAGACCTTTCGGAGGTT

Alignment

ORF - retro_btau_1342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.58 %
• Parental protein coverage: 84.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRKETPPPLV-PPAAREWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWL-FKDPCAAP
          M.KETP..LV.P.........P.....M...LEAA.Y..DG..LL.AS.LS..CWAG.L.L.F......P
Retrocopy MQKETPSFLV>PHPVAKSGTLPLTRLPM*QVLEAALYLFDGMFLLQASNLSDHCWAGPLRL<FQGRFVPP

Parental  NEGFCSAGVQTEAGVADLTWVGDRGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGT
          ..............VA.LTW.GDRGI.VASD.GAVELWELDENETLI..KFCKY.H.DIVSTVSVLSSGT
Retrocopy PRKVSASLESRQRRVANLTWIGDRGIVVASDPGAVELWELDENETLIDNKFCKYKHNDIVSTVSVLSSGT

Parental  HAVS-GSKDFCIKVWDLAQQMVLNSYRAHSGQVTCVAASPHKDSVFLSCGEDNRILLWDTRCPKPASQMG
          .AVS.GSKDF.IKV.DLA.QMV.NSYRAHSGQ.TCVAA..HKD.VFLSCGEDNRI.L.D..CPKPASQMG
Retrocopy QAVS>GSKDFWIKV*DLARQMVQNSYRAHSGQATCVAAFLHKDPVFLSCGEDNRIVLEDICCPKPASQMG

Parental  CSASGYLPTSLTWHPQQSEVFVFGDENGTVSLVDTKSAGCALSSVVHSQCVTGLVFSPHSAPFLASVSED
          ..ASGYL..SL..HPQQ.EVFVFGDENGTV..VDTKSA.CALSSVV.S.C..G.VFSPHSAPFLASVS..
Retrocopy HGASGYLLASLALHPQQTEVFVFGDENGTVPPVDTKSASCALSSVVQS*CISGPVFSPHSAPFLASVSHN

Parental  CSLAVLDSGLSEV
          .SLAVLD..LSEV
Retrocopy YSLAVLDLDLSEV

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	0.00 RPM	5.34 RPM
ERP005899_muscle	0.00 RPM	9.03 RPM
SRP017611_brain	0.00 RPM	9.96 RPM
SRP017611_kidney	0.06 RPM	14.76 RPM
SRP017611_liver	0.00 RPM	6.72 RPM
SRP030211_testis	0.16 RPM	17.82 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1342 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1342 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014102	1 retrocopy	retro_btau_1342 ,
Choloepus hoffmanni	ENSCHOG00000013829	1 retrocopy	retro_chof_2618,
Callithrix jacchus	ENSCJAG00000013344	2 retrocopies	retro_cjac_1166, retro_cjac_3063,
Dasypus novemcinctus	ENSDNOG00000006521	1 retrocopy	retro_dnov_695,
Homo sapiens	ENSG00000116455	1 retrocopy	retro_hsap_2995,
Gorilla gorilla	ENSGGOG00000005208	1 retrocopy	retro_ggor_2076,
Macaca mulatta	ENSMMUG00000003311	1 retrocopy	retro_mmul_1917,
Mus musculus	ENSMUSG00000000561	1 retrocopy	retro_mmus_1120,
Nomascus leucogenys	ENSNLEG00000003918	1 retrocopy	retro_nleu_746,
Oryctolagus cuniculus	ENSOCUG00000007801	1 retrocopy	retro_ocun_535,
Pongo abelii	ENSPPYG00000001033	1 retrocopy	retro_pabe_2482,
Pan troglodytes	ENSPTRG00000001098	1 retrocopy	retro_ptro_2026,
Tupaia belangeri	ENSTBEG00000010325	1 retrocopy	retro_tbel_2253,