RetrogeneDB ID: retro_btau_55

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:3159663..3160998(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000004624
• Aliases: TUBB, TUBB2A
• Status: KNOWN_PROTEIN_CODING

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_55
ATGAGGGAAATCGTGCACATCCAGGCCGGTCAGTGTGGCAATCAGATCGGTGCCAAGTTCTGGGAGGTGATCAGTGATGA
ACATGGCATCGACGCCACCGGCACCTATCATGGGGACAGCGACCTACAACTGGACCGCATCTCCGTGTACTACAATGAAG
CCACAGGTGGCAAATATGTCCCTCGTGCTATCTTGGTGGATCTAGAACCCGGAACCATGGATTCTGTTCACTCAGGTCCT
TTTGGTCAGATCTTCAGATCAGACAACATTGTTTTTGGTCAGTCCGGGGCAGACAACAACTGGGCCAAGGGCCACTATAG
AGAGGGAGCCGAGCTGGTTGACTCGGTCCTGGATGTGGTTCGGAAGGAGGCCAAGAGCTGTGACTGCCTGCAGGGCTTCC
AGCTGACCCACTCGCTGGGTGGGGGCACTGACTCCGGAATGGGCACCTTGCTCATCAGCAAGATCCGTGAAGAGTATCCT
GACCACATCATGAACACCTTCAGCGTGGTGCCCTCACCCAAAGTTTCCGACACTGTGGTTGAGCCCTACAACGCCACCCT
CTCTGTCCATCAGCTGGTGGAGAACACTGATGAAACCTATTGCATTGACAACGAGGCCCTTTACGCCATATGTTTCCGCA
CCCTCAAGCTGACCACACCAACCTATGGAGACCTGAACCAGCTCGTCTCGGCCACCATGAGTGGAGTCACCACTTGCCTC
CGCTTCCCTGGCCAGCTCAATGCTGACCTCCACAAGCTGGCCGTCAACATGGTGCCCTTCCCACACCTCCACTTCTTCGT
GCCTGGCTTTGCCCCTCTAACCAGCTGTGGCAGCCAGCAGTATTGGGCCCTCACTGTCCCTGAGCTCACCCAGCAGGTCT
TCGATGCCAAGAACATGATGGCTGCCTGTGACCCCCGCCATGGCCGGTACCTCACCGTGGCTGCTGTGTTCCGTGGGCAG
ATGTCCATGAAGGAGGTAGATGAGCAGATGCTCAACGTGCAGAATAAGAACAGCAGCTACTTCGTGGAATGGATCCCCAA
CAATGTCAAGACAGCTGTTTGCGACATCCCACCCCGTGGTCTGAAGATGGCAGTCACCTTCATTGGCAACAGCACGGCCA
TCCAGGAGCTGTTCAAGCGCATCTCGGAGCAGTTCATGGCCATGTTCCGCCGGAAGGCCTTCCTCCACTGGTACACAGGT
GAGGGCATGGATGAGACGGAGTTCACCGAGGCTGAGAGCAACATGAACGACCTCGTCTCCGAGTACCAGCAGTACCAGGA
TGCCACCGCAGAAGAGGAAGAGGATTTCGGTGAGGAGGCCGAAGAGGAGGCCTAA

Alignment

ORF - retro_btau_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.72 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
          MREIVHIQAGQCGNQIGAKFWEVISDEHGID.TGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
Retrocopy MREIVHIQAGQCGNQIGAKFWEVISDEHGIDATGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
          GTMDSV.SGPFGQIFR.DN.VFGQSGA.NNWAKGHY.EGAELVDSVLDVVRKEA.SCDCLQGFQLTHSLG
Retrocopy GTMDSVHSGPFGQIFRSDNIVFGQSGADNNWAKGHYREGAELVDSVLDVVRKEAKSCDCLQGFQLTHSLG

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          GGT.SGMGTLLISKIREEYPD.IMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY.I
Retrocopy GGTDSGMGTLLISKIREEYPDHIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYAI

Parental  CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ
          CFRTLKLTTPTYGDLN.LVSATMSGVTTCLRFPGQLNADL.KLAVNMVPFP.LHFF.PGFAPLTS.GSQQ
Retrocopy CFRTLKLTTPTYGDLNQLVSATMSGVTTCLRFPGQLNADLHKLAVNMVPFPHLHFFVPGFAPLTSCGSQQ

Parental  YRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVK
          Y.ALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRG.MSMKEVDEQMLNVQNKNSSYFVEWIPNNVK
Retrocopy YWALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGQMSMKEVDEQMLNVQNKNSSYFVEWIPNNVK

Parental  TAVCDIPPRGLKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
          TAVCDIPPRGLKMAVTFIGNSTAIQELFKRISEQF.AMFRRKAFLHWYTGEGMDE.EFTEAESNMNDLVS
Retrocopy TAVCDIPPRGLKMAVTFIGNSTAIQELFKRISEQFMAMFRRKAFLHWYTGEGMDETEFTEAESNMNDLVS

Parental  EYQQYQDATAEEEEDFGEEAEEEA
          EYQQYQDATAEEEEDFGEEAEEEA
Retrocopy EYQQYQDATAEEEEDFGEEAEEEA

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	0.63 RPM	410.54 RPM
SRP017611_brain	2.51 RPM	159.56 RPM
SRP017611_kidney	0.00 RPM	103.07 RPM
SRP017611_liver	1.06 RPM	51.35 RPM
SRP030211_testis	0.09 RPM	59.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_55 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_55 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_55 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,