RetrogeneDB ID: retro_btau_929

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 21:25623158..25624469(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.53243
• Ensembl ID: ENSBTAG00000001489
• Aliases: None
• Description: tubulin alpha-1B chain [Source:RefSeq peptide;Acc:NP_001159977]

Sequence

>retro_btau_929
TGCGTGTGAGTGCATCTCCAGGCTGGTGTCCAGATCAGCAATGCCTGCTGGGAGCTCTACTGCCTGGAACACGGCATTCA
GCCTGATGGCCAGATGCCAAGTGACAAGATTATTGGGGGAGGAGACGACTCCTTCAACACCTTCTTCAGTGAGACAGGGG
CTGGCAAGCATGTGCCCAGGGCAGTGTTTGTCGACCTGGAACCCACAGTCATTGATGAGGTTCGCACCGGCACCTACCAC
CAGCTCTTCCACCCTGAACAGCTCATCACAGGCAAAGAAGATGCCACCAATAATTAGGCCCGAGGTCACTACACCATTGG
CAAGGAGATCATTGACCTCGTCTTGGACCGAATTTGGAAACTGGCTGACCAGTGCACAGGTCTTCAGGGCTTCTTGGTTT
TCCAGAGCTTTGGTGGGGGAACTGGTTCTGGGTTTACCTCCCTGCTGATGGAATGTCTTTCAGTCGATTATGGAAAGAAA
TCCAAGCTGGAGTTCTCCATTTACCCAGCCCCCCAGGTTTCCACAGCTGTCGTTGAGCCCTACAACTCCATCCTCACCAC
CCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTCATAGAAACCTTG
ACATTGAGCGCCTGACATATACTAACTTGAATAGGTTGATAGGTCAAATTGTGTCCTCCACCACTGCTTCCCTGAGGTTT
GATGGCACCCTGAATGTGGATCTGACAGAGTTCCAGACCAACCTGGTGCCCTATCCCCGCATCCACTTCCCTCTGGCCAC
ATACGCCCCCGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATGCTTGCTTTGAGC
CAGCCAACCAGATGGTGAAATGTGACCCTCGCCATGGTAAATACATGGCCTGCTGCCTGTTGTACTGTGGTGACATGGTT
CCCAAAGATGTCAGTGCTGCCATTGCCACCATCAAGACCAAGCGTACCATCCAGTTTGTGGACTGGTGCCCCATTGGCTT
CAAGGTTGGCATTAACTACCAGCCTCCCACTGTGGTACCTGGTGGAGACCTGGCCAAAGTACAGCGAGCTGTGTGCATGC
TAAGCAACACCACAGCCATCACTGAGGCCTGGGCTCGCCTGGACCACAAGTTGGACCTGATGTATGCCAAGCGTGCCTTT
GTTCACTGGTACGTGGGTGAGGGCATGGAGGAAGGAGAGTTTTCTGAGGCCCGTGAAGACATGGTTGCCCTTGAGAAGGA
TTATGAGGAGGTTGGTGTGGATTCTGTGGAA

Alignment

ORF - retro_btau_929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.52 %
• Parental protein coverage: 97.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPT
          C...H..QAGVQI.NACWELYCLEHGIQPDGQMPSDK.IGGGDDSFNTFFSETGAGKHVPRAVFVDLEPT
Retrocopy CV*VHL-QAGVQISNACWELYCLEHGIQPDGQMPSDKIIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPT

Parental  VIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGG
          VIDEVRTGTY.QLFHPEQLITGKEDA.NN.ARGHYTIGKEIIDLVLDRI.KLADQCTGLQGFLVF.SFGG
Retrocopy VIDEVRTGTYHQLFHPEQLITGKEDATNN*ARGHYTIGKEIIDLVLDRIWKLADQCTGLQGFLVFQSFGG

Parental  GTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDIC
          GTGSGFTSLLME.LSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDIC
Retrocopy GTGSGFTSLLMECLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDIC

Parental  RRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYH
          .RNLDIER.TYTNLNRLIGQIVSS.TASLRFDG.LNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYH
Retrocopy HRNLDIERLTYTNLNRLIGQIVSSTTASLRFDGTLNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYH

Parental  EQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKV
          EQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLY.GD.VPKDV.AAIATIKTKRTIQFVDWCP.GFKV
Retrocopy EQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYCGDMVPKDVSAAIATIKTKRTIQFVDWCPIGFKV

Parental  GINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEARE
          GINYQPPTVVPGGDLAKVQRAVCMLSNTTAI.EAWARLDHK.DLMYAKRAFVHWYVGEGMEEGEFSEARE
Retrocopy GINYQPPTVVPGGDLAKVQRAVCMLSNTTAITEAWARLDHKLDLMYAKRAFVHWYVGEGMEEGEFSEARE

Parental  DMAALEKDYEEVGVDSVE
          DM.ALEKDYEEVGVDSVE
Retrocopy DMVALEKDYEEVGVDSVE

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	3.53 RPM
ERP005899_muscle	0.16 RPM	20.96 RPM
SRP017611_brain	0.23 RPM	359.36 RPM
SRP017611_kidney	0.12 RPM	19.68 RPM
SRP017611_liver	0.15 RPM	4.68 RPM
SRP030211_testis	0.05 RPM	77.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_929 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_929 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_929 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929 ,
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus	ENSDNOG00000004121	1 retrocopy	retro_dnov_43,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223,
Homo sapiens	ENSG00000167552	1 retrocopy	retro_hsap_3313,
Nomascus leucogenys	ENSNLEG00000017836	2 retrocopies	retro_nleu_245, retro_nleu_2757,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72,