RetrogeneDB ID: retro_btau_1570

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:39834210..39835087(-)
• Located in intron of: ENSBTAG00000001707

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.52587
• Ensembl ID: ENSBTAG00000014159
• Aliases: None
• Description: tubulin--tyrosine ligase [Source:RefSeq peptide;Acc:NP_001106704]

Sequence

>retro_btau_1570
ATGTACACCTTTGTGGTGCGCGATGGGAACAGCAGCGTCTATGCCAATGAGGTGTTCTGGCTGCTGCTCGCCACAGGCCA
CTGGAAGCGGCTGCAATGGGATAACCCCAGGTTCAGCCTGATGCTGGAAGAAAGAAACCGGCTGCCCTTCAGGAGACTGG
ATCGTGAGCCTGGCTGATGCACTTGGTGAATTACTACAGAGGGGCCGACAAACTGTGTCGCAAAGCATCTTTAGTGAAGC
TCATCAAAACCAGCCCAGAACAGGCTGAGTCCTGCACATGGTTCCGCGAGTCCTATGTGATTTATCCAACCAACCTTAAG
ACCCTAGTTGCTCCAGCTCAGAATGGAATCCATCCACTGCTCCGTAGTTCAAGGACAGACGACAGAGAATTTTTTCTGAC
TTAATATAACAGAAAGAAAGAGGAGGGAGAGGGCAACGCTTGGATTGCAAAGTCATCAGCCGGAGCCAAAGGTGAAGGCA
TACTCATCTTCTCAGAAGCTACAGAACTGTTGGATTTCATAGACAACCAAGGCCAGATGCACGTGATCCAGAAATACCTG
GAGCTCCCGTTGTTCCTGGAAGCCTGGTCATCGCAAGTTTGACATCTGAGGCTGGGTCTTGGTGGACTGTCAGTTTAATA
TCTACCTCTATAGTGAGGGTGTCCTGCAGACTGCTTCAGAACCGTATCAGGTGGATTATTTCCAAGATAAAACCAGCCAC
TTGACTAATCACTGCATTCAAAAGGAGTACTCAGAGAACTATGGGAAGTATGAAGAAGGGGAACGCAATGTTCTTTGAGG
AATTCAATCAGTACCTAACAAGTGCTTTGAACATCACCCTGGAAAGTAGTATCTTACTACAAATCAAAGGTATCATA

Alignment

ORF - retro_btau_1570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.42 %
• Parental protein coverage: 77.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MYTFVVRDENSSVYA-EVSRLLLATGHWKRLRRDNPRFNLMLGERNRLPFGRLGHEPG-LMQLVNYYRGA
          MYTFVVRD.NSSVYA.EV..LLLATGHWKRL..DNPRF.LML.ERNRLPF.RL..EPG.LM.LVNYYRGA
Retrocopy MYTFVVRDGNSSVYANEVFWLLLATGHWKRLQWDNPRFSLMLEERNRLPFRRLDREPG<LMHLVNYYRGA

Parental  DKLCRKASLVKLIKTSPELAESCTWFPESYVIYPTNLKTPVAPAQNGIHPPLHSSRTDEREFFLASYNRK
          DKLCRKASLVKLIKTSPE.AESCTWF.ESYVIYPTNLKT.VAPAQNGIHP.L.SSRTD.REFFL..YNRK
Retrocopy DKLCRKASLVKLIKTSPEQAESCTWFRESYVIYPTNLKTLVAPAQNGIHPLLRSSRTDDREFFLT*YNRK

Parental  KEEGEGNVWIAKSSAGAKGEGILISSDATELLDFIDNQGQVHVIQKYLERPLLLE-PGHRKFDIRSWVLV
          KEEGEGN.WIAKSSAGAKGEGILI.S.ATELLDFIDNQGQ.HVIQKYLE.PL.LE.PGHRKFDI..WVLV
Retrocopy KEEGEGNAWIAKSSAGAKGEGILIFSEATELLDFIDNQGQMHVIQKYLELPLFLE>PGHRKFDI*GWVLV

Parental  DHQFNIYLYREGVLRTASEPYHMDNFQDKTCHLTNHCIQKEYSKNYGKYEE-GNEMFFEAFNRYLTSALN
          D.QFNIYLY.EGVL.TASEPY..D.FQDKT.HLTNHCIQKEYS.NYGKYEE.GN.MFFE.FN.YLTSALN
Retrocopy DCQFNIYLYSEGVLQTASEPYQVDYFQDKTSHLTNHCIQKEYSENYGKYEE>GNAMFFEEFNQYLTSALN

Parental  ITLESSILLQIKHII
          ITLESSILLQIK.II
Retrocopy ITLESSILLQIKGII

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	0.14 RPM
ERP005899_muscle	0.16 RPM	4.70 RPM
SRP017611_brain	0.00 RPM	40.97 RPM
SRP017611_kidney	0.00 RPM	8.71 RPM
SRP017611_liver	0.00 RPM	1.66 RPM
SRP030211_testis	0.07 RPM	1.52 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1570 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1570 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014159	1 retrocopy	retro_btau_1570 ,