RetrogeneDB ID: retro_btau_1087

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 25:17044369..17045680(-)
• Located in intron of: ENSBTAG00000016505

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.92088
• Ensembl ID: ENSBTAG00000014827
• Aliases: None
• Description: ubiquilin-1 [Source:RefSeq peptide;Acc:NP_777053]

Sequence

>retro_btau_1087
ATGGCCGAGAATAGTGAAAGCGGCGGCCCTCCGAGTTCCCAGGACAACGCCGCCGCGGCCGAAGGTGCCGGCGCCCCTGC
CGCCACCGCCTCCACGGAACCCAAGATCATGAAAGTCACCGTGAAGACCCCGAAGGAGAAGGAGGAGTTCGCAGTGCCCG
AGAACAGCTCTGTCCAGCAGTTCAAGGAAGAAATCTCGAAACGTTTCAAATCACATACCGACCAACTTGTGTTGATATTT
GCGGGAAAAATTTTAAAAGATCAAGATACTTTGAGTCAGCATGGAATTCACGATGGACTTACTGTTCACCTTGTCATCAA
AACACAAAACAGGCCTCAGGATCATTCAGCTCAACAAACAAATGCCAGTGGAACCAGTGCTACCACATCATCAGCTCCTA
GTAGTAACTCCACATCTGGTTCTGCCACTAGCAGCCCTTTTGGTTTAGGTGGCCTTGGAGGACTTGCAGGTCTGAGTAGC
TTGGGTTTGAATACTACCAACTTCTCTGAACTACAGAGCCAGATGCAGCGGCAACTTATGTCCAATCCTGAAATGATGGT
CCAGATCATGGAGAATCCCTTTGTCCAGAGCATGCTTTCAAATCCTGACCTGATGAGGCAGTTAATTATGGCCAATCCAC
AAATGCAACAGTTGATACAGAGAAATCCAGAAATTAGTCATATGCTAAATAATCCAGATATTATGAGACAAACATTGGAA
CTTGCTAGGAATCCGGCAATGATGCAGGAAATGATGAGAAACCAGGACCGAGCCTTGAGCAACCTGGAAAGCATCCCAGG
GGGATACAATGCTTTACGGCGCATGTACACAGATATTCAGGAACCCATGTTGAGTGCTGCACAAGAACAGTTTGGTGGTA
ATCCGTTTGCTTCGTTAGTGAGCAATACATTGTCAGGTGAAGGTAGTCAGCCTTCCCGTACAGAAAATAGAGATCCATTA
CCCAATCCGTGGGCTCCACAGGCTTCTCAGAGTTCATCAGCTTCCAGTGGCACCACCAGCTCAGTGGGGGGCACTAGTGG
TAGTGCTGCTGGTGGTACTGCTGGGCAGAGTTCTGCTGCGCCAAATTTGGGACCTGGAGTAGGAGCCAGTATGTTCAATA
CACCAGGAATGCAGAGCTTGTTGCAGCAAATAACTGAAAACCCACAACTTATGCAAAACATGTTGTCTGCCCCCTACATG
AGAAGCATGATGCAGTCACTAAGCCAGAACCCTGACCTTGCTGCACAGATGCAGAATCCTGATACGTTATCGGCTATGTC
AAACCCTAGAGCAATGCAGGCCTTATTACAG

Alignment

ORF - retro_btau_1087 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.34 %
• Parental protein coverage: 74.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAENSESGGPPSSQDNAAAAEGAGAPAATASTEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK
          MAENSESGGPPSSQDNAAAAEGAGAPAATASTEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK
Retrocopy MAENSESGGPPSSQDNAAAAEGAGAPAATASTEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK

Parental  SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNASGTSATTSSAPSSNSTSG
          SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNASGTSATTSSAPSSNSTSG
Retrocopy SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNASGTSATTSSAPSSNSTSG

Parental  SATSSPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLMSNPEMMVQIMENPFVQSMLSNPDLMRQLIM
          SATSSPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLMSNPEMMVQIMENPFVQSMLSNPDLMRQLIM
Retrocopy SATSSPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLMSNPEMMVQIMENPFVQSMLSNPDLMRQLIM

Parental  ANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQ
          ANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQ
Retrocopy ANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQ

Parental  EPMLSAAQEQFGGNPFASLVSNTSSGEGSQPSRTENRDPLPNPWAPQASQSSSASSGTTSSVGGTSGSAA
          EPMLSAAQEQFGGNPFASLVSNT.SGEGSQPSRTENRDPLPNPWAPQASQSSSASSGTTSSVGGTSGSAA
Retrocopy EPMLSAAQEQFGGNPFASLVSNTLSGEGSQPSRTENRDPLPNPWAPQASQSSSASSGTTSSVGGTSGSAA

Parental  GGTAGQSSAAPNLGPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMMLN
          GGTAGQSSAAPNLGPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQM...
Retrocopy GGTAGQSSAAPNLGPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMQNP

Parental  NPLFA-GNPQLQEQMRQ
          ..L.A..NP.......Q
Retrocopy DTLSAMSNPRAMQALLQ

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	0.72 RPM	30.28 RPM
ERP005899_muscle	1.74 RPM	67.15 RPM
SRP017611_brain	2.19 RPM	78.52 RPM
SRP017611_kidney	2.25 RPM	96.91 RPM
SRP017611_liver	1.59 RPM	53.76 RPM
SRP030211_testis	5.74 RPM	102.46 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1087 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1087 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014827	2 retrocopies	retro_btau_1087 , retro_btau_188,
Canis familiaris	ENSCAFG00000001435	1 retrocopy	retro_cfam_236,
Callithrix jacchus	ENSCJAG00000003609	2 retrocopies	retro_cjac_3977, retro_cjac_4067,
Cavia porcellus	ENSCPOG00000004849	1 retrocopy	retro_cpor_113,
Dasypus novemcinctus	ENSDNOG00000012687	1 retrocopy	retro_dnov_14,
Dipodomys ordii	ENSDORG00000015266	1 retrocopy	retro_dord_680,
Equus caballus	ENSECAG00000019110	1 retrocopy	retro_ecab_1063,
Echinops telfairi	ENSETEG00000002822	1 retrocopy	retro_etel_39,
Felis catus	ENSFCAG00000015049	1 retrocopy	retro_fcat_83,
Homo sapiens	ENSG00000135018	1 retrocopy	retro_hsap_58,
Myotis lucifugus	ENSMLUG00000002036	2 retrocopies	retro_mluc_1774, retro_mluc_33,
Mustela putorius furo	ENSMPUG00000002028	1 retrocopy	retro_mputfur_55,
Mus musculus	ENSMUSG00000005312	1 retrocopy	retro_mmus_83,
Nomascus leucogenys	ENSNLEG00000003306	1 retrocopy	retro_nleu_31,
Otolemur garnettii	ENSOGAG00000012947	1 retrocopy	retro_ogar_276,
Pongo abelii	ENSPPYG00000019323	1 retrocopy	retro_pabe_87,
Pan troglodytes	ENSPTRG00000021055	1 retrocopy	retro_ptro_93,
Rattus norvegicus	ENSRNOG00000019282	1 retrocopy	retro_rnor_339,
Ictidomys tridecemlineatus	ENSSTOG00000013462	1 retrocopy	retro_itri_157,
Tursiops truncatus	ENSTTRG00000004696	1 retrocopy	retro_ttru_1475,