RetrogeneDB ID: retro_btau_687

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:9317789..9318653(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.87811
• Ensembl ID: ENSBTAG00000014741
• Aliases: None
• Description: homeobox protein OTX2 [Source:RefSeq peptide;Acc:NP_001180130]

Sequence

>retro_btau_687
ATGATGTCTTATCTTAAGCAACCGCCTTATGCAGTCAGTGGGTTGAGTCTGACCACTCGGGCATGGACTTGCTGCACCCC
TCGGTGGGCTCCCCAGCCACCCCTTGGAAACACTGGCAGGAGAGGACGATGTTCACCCGAGTGCAGCTGGATATGCTGGA
AGCACTGTTTGCTAAGACCTGATACCCACACATCTTCACGTGGGAGGAGGTGGCACTGAAAATCAACTTGCCTGAGTCCA
GGGTACAGGCATGGTTTAAGAATCAAAGAGCGAAGTGCCGCCAACAGGGGCAGCAGCAGCAGAATGGAGGTCAAAACAAA
GTGAGACCTGCCAAAAAGAAGACATCTCCTGCCTGGGAAGTGATTTCAGAGGGTGGAACAAGTGGCCAGATCACTCCCCC
TTCTAGCACCTCAGTCCCAGTCATTTCCAGCAGCAGTGCTCCTCCATCTGTCTGGAGCCCAGCCATCCCCCCATTGTCAG
ATCCCCCATCCACCTCCTCTCCCTGCATGCAGAGGTCCTACCCCATGACCTATACTGAGGCTTCAGGTCATAGTCAAGGA
TATGCTGGCTCAGTTTCCTACTTTGGGGGGCATGGACTGTGGATCTTATTTGAGCCCTGTGCATCACCAGCTTCCTGGAC
CAGGGACTGCACTCAGTCCCATGGGTACCAATGCAGTCACCAGCCATCTCAATCAGTCCCCAGCTTCTGTTTTCACCCAG
GGATGTGGAGCTTTAAGCTTGGGTTTTAACTCAACCACGGATTGCTTGGATTATAAGGACCAAACTGCCTCCTGGAAACT
TAACTTCAATGCTGACTGCTTAGATTATAAAGATCAGACATCTTCGTGGAAATTCCAGGTTTTG

Alignment

ORF - retro_btau_687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMSYLKQPPYAVNGLSLTT-SGMDLLHPSVGYPATPRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMRE
          MMSYLKQPPYAV.GLSLTT.SGMDLLHPSVG.PATP.K...ERT.FTR.QLD.LEALFAKT.YP.IF..E
Retrocopy MMSYLKQPPYAVSGLSLTT<SGMDLLHPSVGSPATPWKHWQERTMFTRVQLDMLEALFAKT*YPHIFTWE

Parental  EVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGGQNKVRPAKKKTSPAREVSSESGTSGQFTPPSSTSV
          EVALKINLPESRVQ.WFKN.RAKCRQQ.QQQQNGGQNKVRPAKKKTSPA.EV.SE.GTSGQ.TPPSSTSV
Retrocopy EVALKINLPESRVQAWFKNQRAKCRQQGQQQQNGGQNKVRPAKKKTSPAWEVISEGGTSGQITPPSSTSV

Parental  PAISSSSAPVSIWSPASISPLSDPLSTSSSCMQRSYPMTYTQASGYSQGYAGSTSYF-GGMDCGSYLTPM
          P.ISSSSAP.S.WSPA.I.PLSDP.STSS.CMQRSYPMTYT.ASG.SQGYAGS.SYF.GGMDCGSYL.P.
Retrocopy PVISSSSAPPSVWSPA-IPPLSDPPSTSSPCMQRSYPMTYTEASGHSQGYAGSVSYF>GGMDCGSYLSPV

Parental  HHQLPGPGTTLSPMGTNAVTSHLNQSPASLSTQGYGASSLGFNSTTDCLDYKDQTASWKLNFNADCLDYK
          HHQLPGPGT.LSPMGTNAVTSHLNQSPAS..TQG.GA.SLGFNSTTDCLDYKDQTASWKLNFNADCLDYK
Retrocopy HHQLPGPGTALSPMGTNAVTSHLNQSPASVFTQGCGALSLGFNSTTDCLDYKDQTASWKLNFNADCLDYK

Parental  DQTSSWKFQVL
          DQTSSWKFQVL
Retrocopy DQTSSWKFQVL

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	0.00 RPM
ERP005899_muscle	0.00 RPM	0.00 RPM
SRP017611_brain	0.00 RPM	3.06 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.00 RPM	0.08 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_687 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_687 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014741	1 retrocopy	retro_btau_687 ,
Callithrix jacchus	ENSCJAG00000018583	1 retrocopy	retro_cjac_1380,
Cavia porcellus	ENSCPOG00000003420	1 retrocopy	retro_cpor_149,
Sus scrofa	ENSSSCG00000005063	1 retrocopy	retro_sscr_417,
Tursiops truncatus	ENSTTRG00000004650	1 retrocopy	retro_ttru_473,