RetrogeneDB ID: retro_btau_856

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:11546914..11547811(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NHEJ1
• Ensembl ID: ENSBTAG00000031041
• Aliases: None
• Description: non-homologous end-joining factor 1 [Source:RefSeq peptide;Acc:NP_001068861]

Sequence

>retro_btau_856
ATGGAGGAACTGGAGCAAGACTTGCTGATGCAGTCATGTGCACGGCTACAGCTTGCCGAGAACTCCCTCCTGGCCAAGGC
CTATATCACCAGGCAGGGCTATGCCATGCTGGTTTCAGATCTTTAACAAGTGTGGCAAGGACAGGTGTACACTAGTGCGA
TCAGTCAGCGAGCCAAGGAGCTGAACAAGCACCTGACTGCTCCTCCCAAGGCTTTTCTTTGACATTTGGATGATCTGCTT
TTCCCACTGTTGAAGGATGCTTCTTGCCCTGGCATAGCTGCATTCTCCTGTGATTGTGTGGCAGAGGCACTGACACTATG
GAGGCAGAGTGAGCTTTCTGGCCTCCCATTCTACTGGAATTTCCACTGCACCCTAGCTAGCCCTTTGGTGGTCTCCTAAT
GTTTGATTCGTCCTCTGATGGGCATGAGTCTGGCATTGCAGTGCCAGGTGAGTGACCTAACAATGATGCTTCACATGATA
GATCTAGAGATCCAGGACTACCAGGAGAATGGGGCTATGCTGAGCCAAAACTGGTTGAAGACAGAGCCATTTGAATAGAC
TTTCTTCTTGGAACAATTTATGGTGGAGAAACTACCAGAGGCATGCGGTGTTGGTGATAGAAGACCCTTCATCACAAATC
TGCAGAGTCTGGATATGGCAGTCACCAGATAAAAGATCCAGGTGGGACAGAAACATCAGGGTGCTGGAGATCCCCAGACC
TCAAGCAGTGCCTTCTCACAGGGAACTGATAACCAACTTCTGAATCAGCCAGAAGAGCCTATCTCCTCAGCACCATCCCT
CCCAGGACCTGAGAAGGAGCCCACAGTTCCTTCAGCCCAATGCAGAGACCTCAGCTCTTTGAAAGTGCAGAGGAAGAAGC
TAACAGGGCTCTTCAGT

Alignment

ORF - retro_btau_856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEELEQGLLMQPWAWLQLAENSLLAKAYITRQGYALLVSDLQQVWHEQVDTSVISQRAKELNKRLTAPPE
          MEELEQ.LLMQ..A.LQLAENSLLAKAYITRQGYA.LVSDL.QVW..QV.TS.ISQRAKELNK.LTAPP.
Retrocopy MEELEQDLLMQSCARLQLAENSLLAKAYITRQGYAMLVSDL*QVWQGQVYTSAISQRAKELNKHLTAPPK

Parental  AFLRHLDDLLRPLLKDASCPGTATFSCDRVAEALILQVRSELSGLPFYWNFHCILASPSLVSQHLIRPLM
          AFL.HLDDLL.PLLKDASCPG.A.FSCD.VAEAL.L...SELSGLPFYWNFHC.LASP..VS..LIRPLM
Retrocopy AFL*HLDDLLFPLLKDASCPGIAAFSCDCVAEALTLWRQSELSGLPFYWNFHCTLASPLVVS*CLIRPLM

Parental  GMSLALQCQVRDLTTLLHMKDLEIQDYQESGATLSRDRLKTEPFEESSFLEQFMVEKLPEACSVGDGRPF
          GMSLALQCQV.DLT..LHM.DLEIQDYQE.GA.LS...LKTEPFE...FLEQFMVEKLPEAC.VGD.RPF
Retrocopy GMSLALQCQVSDLTMMLHMIDLEIQDYQENGAMLSQNWLKTEPFE*TFFLEQFMVEKLPEACGVGDRRPF

Parental  IANLQSMYMAVTRQAIQVGQKHHDTGDPHTSSSAFSQGTDNQRLNQLEEPVSSTPSLPGPETEPTVSS-G
          I.NLQS..MAVTR..IQVGQKH...GDP.TSSSAFSQGTDNQ.LNQ.EEP.SS.PSLPGPE.EPTV.S..
Retrocopy ITNLQSLDMAVTR*KIQVGQKHQGAGDPQTSSSAFSQGTDNQLLNQPEEPISSAPSLPGPEKEPTVPS<S

Parental  PMQKPQL-LKVKRKKLRGLFS
          PMQ.PQL.LKV.RKKL.GLFS
Retrocopy PMQRPQL>LKVQRKKLTGLFS

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	5.05 RPM
ERP005899_muscle	0.00 RPM	14.31 RPM
SRP017611_brain	0.00 RPM	1.96 RPM
SRP017611_kidney	0.00 RPM	13.57 RPM
SRP017611_liver	0.00 RPM	2.87 RPM
SRP030211_testis	0.05 RPM	2.67 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_856 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_856 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031041	1 retrocopy	retro_btau_856 ,
Tursiops truncatus	ENSTTRG00000010020	1 retrocopy	retro_ttru_1833,