RetrogeneDB ID: retro_btau_471

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:50509650..50510980(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB5
• Ensembl ID: ENSBTAG00000006969
• Aliases: TUBB, TUBB2A, TUBB2B, TUBB5
• Description: Tubulin beta-5 chain [Source:UniProtKB/Swiss-Prot;Acc:Q2KJD0]

Sequence

>retro_btau_471
ATGAGGGAAATCGTGCACATCCAGGCCGGTCAGTGTGGCAATCAGATCAGTGCCAAGTTCTGGGAGGTGATCAGTGATGA
ACATGGCATCAACCCCACCGGCACCTATCATGGGGACAGCAACCTGCAGCTGGACTGCATCTCCGTGTAATACAATGAAG
CCACAGGTGGCAAATATGTCCCTTGTGCTATCTTGGTGATCTAGAACCCAGAACCATGGACTCTGTTCGCTCAGGTCCTT
TTGGTCAGATCTTCAGACCAGACAACTTTGTTTTTGGTCAGTCCGGGGCAGGCAACAACTGGGCCAAGGGCCACTATACA
GAGGGAGCCAAGCTGGTTGACTCGGTCCTGGATGTGGTTCGGAAGGAGGCCAAGAGCTGTGACTGCCTGCAGGGCTTCCA
GCTGACCCACTCGCTGGGTGGGGGCACTGGCTCCGGAATGGGCACCTTGCTCATCAGCAAGATCCGTGAAGAGTATCCTG
ACCGCATCATGAACACCTTCAGCATGGTGCCCTCACCCAAAGTGTCCAACACTGTGGTTGAGCCCTACAACGCCACCTTC
TCTGTCCATCAGCTGGTGGAGAACACTGATGAAACCTACTGCATTGAGAACGAGGCCCTTTACAACATATGTTTCCACAC
CCTCAGGCTGACTGTGCCAACCTACGGAGACCTGAACCACCTCGTCTTGGCCACATGAGTGGAGTCACCACTTGCCTCCA
CTTCCCTGGCCAGCTCAATGCTAACCTCCGCAAGCTGGCCTTCAACATGGTGCCCTTCCCACGCCTCCACTTCTTCGTGC
CTGGCTTTGCCCCTCTAACCAGCCATGGCAGCCAGCAGTATCGGGCCCTCACTGTCCCTGAGCTCACCCAGCAGGTCTTC
GATGCCAAGAACATGATGGCTGCCTGTGACCCCCACCATGGCCGGTACCTCAGCATGGCTGCTGTGTTCTGTGAGCAGAT
GTCCATGAAGGAGGTGGATGAGCAGATGCTCAACGTGCAGAACAAGAACAGGAGCTACTTTATGGAATGGATCCCCAACA
GCGCCAAGACAGCTGTTTGCGACATCCCACCCCGTGGTCTCAAGATGGCAGTCACCTTCATTGGCAACAGCATGGCCATC
CAGGAGCTGTTCAAGTGTATTTCAGAGCAGTTCACGGCCATTTTCTGCCGGAAGGCCTTCCTCCACGGGTACACAGGTGA
GGGCATGGACGAGATGGAGTTCACCGAGGCTGAGAGCAACATGAACGACCTCGTCTCCAAGTACCAGCAGTACCAGGATG
CCACCGCAGAAGAGGAAGAGGATTTCAGTGAGGAGGCCGAAGAGAAGGCC

Alignment

ORF - retro_btau_471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.36 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILV-DLE
          MREIVHIQAGQCGNQI.AKFWEVISDEHGI.PTGTYHGDS.LQLD.ISV.YNEATGGKYVP.AILV.DLE
Retrocopy MREIVHIQAGQCGNQISAKFWEVISDEHGINPTGTYHGDSNLQLDCISV*YNEATGGKYVPCAILV<DLE

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          P.TMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGA.LVDSVLDVVRKEA.SCDCLQGFQLTHSL
Retrocopy PRTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAKLVDSVLDVVRKEAKSCDCLQGFQLTHSL

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYD
          GGGTGSGMGTLLISKIREEYPDRIMNTFS.VPSPKVS.TVVEPYNAT.SVHQLVENTDETYCI.NEALY.
Retrocopy GGGTGSGMGTLLISKIREEYPDRIMNTFSMVPSPKVSNTVVEPYNATFSVHQLVENTDETYCIENEALYN

Parental  ICFRTLKLTTPTYGDLNHLVSAT-MSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGS
          ICF.TL.LT.PTYGDLNHLV.AT.MSGVTTCL.FPGQLNA.LRKLA.NMVPFPRLHFF.PGFAPLTS.GS
Retrocopy ICFHTLRLTVPTYGDLNHLVLAT<MSGVTTCLHFPGQLNANLRKLAFNMVPFPRLHFFVPGFAPLTSHGS

Parental  QQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNN
          QQYRALTVPELTQQVFDAKNMMAACDP.HGRYL..AAVF...MSMKEVDEQMLNVQNKN.SYF.EWIPN.
Retrocopy QQYRALTVPELTQQVFDAKNMMAACDPHHGRYLSMAAVFCEQMSMKEVDEQMLNVQNKNRSYFMEWIPNS

Parental  VKTAVCDIPPRGLKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDL
          .KTAVCDIPPRGLKMAVTFIGNS.AIQELFK.ISEQFTA.F.RKAFLH.YTGEGMDEMEFTEAESNMNDL
Retrocopy AKTAVCDIPPRGLKMAVTFIGNSMAIQELFKCISEQFTAIFCRKAFLHGYTGEGMDEMEFTEAESNMNDL

Parental  VSEYQQYQDATAEEEEDFGEEAEEEA
          VS.YQQYQDATAEEEEDF.EEAEE.A
Retrocopy VSKYQQYQDATAEEEEDFSEEAEEKA

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	12.18 RPM
ERP005899_muscle	0.21 RPM	410.54 RPM
SRP017611_brain	0.05 RPM	159.56 RPM
SRP017611_kidney	0.00 RPM	103.07 RPM
SRP017611_liver	0.08 RPM	51.35 RPM
SRP030211_testis	0.47 RPM	59.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_471 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_471 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006969	2 retrocopies	retro_btau_471 , retro_btau_55,
Canis familiaris	ENSCAFG00000000443	1 retrocopy	retro_cfam_1860,
Echinops telfairi	ENSETEG00000013572	1 retrocopy	retro_etel_641,
Macaca mulatta	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
Mustela putorius furo	ENSMPUG00000011690	3 retrocopies	retro_mputfur_1123, retro_mputfur_607, retro_mputfur_807,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498,
Otolemur garnettii	ENSOGAG00000032213	1 retrocopy	retro_ogar_2391,
Pongo abelii	ENSPPYG00000016419	4 retrocopies	retro_pabe_2920, retro_pabe_3210, retro_pabe_3698, retro_pabe_467,