RetrogeneDB ID: retro_btau_598

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:42515030..42516392(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000038174
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GIN1
• Ensembl ID: ENSBTAG00000021471
• Aliases: None
• Description: Gypsy retrotransposon integrase-like protein 1 [Source:UniProtKB/Swiss-Prot;Acc:A4FUB7]

Sequence

>retro_btau_598
GAAGAAAAAAATAAAGTCCTAAGAGAATGTCATGAAAATGACACTGGAGCCCATCATGGCATATCCAGAACCCTTACTCT
AGTGGAATCCAGTTACTACTGGACTTCTGTGACCAATGATGTCAAACAGTGGGTATATGCTTGTCAGCATTGCCAAGTGG
CAAAAAATACAGTTATTCTAGCACCTAAACAGCACCTTCTCAAAGTGGAGAATCCATGGAGTATAGTTACTGTTGATCTG
ATGGGCCCATTTCATACAAGCAACAGAAGTCATGTATATGCTATAATCATGACAGATTTGTTCACAAAATGGGTTGTGAT
TTTGCCTCTTTGGGATGTTTCAGCATCAGAAATTTCTAAAGCTAGTATCAACATATTTTTCTTATATGGGCCTCCTCAGA
AAATAATAATGGACCAAAGAGATGAATTCATTCATCAGATCAATGTAGAGCTATGTGAATTGTTTGGCACAAAGCAAATT
GTTATTTCTCATGCCTCCCAAACAATTAATCCAGCTGAAAGTACACCTAGCACTATCAAAACCTTTCTTTCCAAACATTG
TGCGGACTACCCAAACGACTGGGATGACCACCTGCCAGCTGTTTCATTCGCCTTCAATGTCACTCACTTTGAACCTACTA
AAAATACACCATATTTTCAAATGTTTAATCGAAATCTTTACATGCCTGAATCTTCAGATATTCATGAAGTGGATGGTGAT
AATACAAGTATGTTTGCCAAAATTCTAGATGCAATTAAAGAAGCTGATAAAATAATGGAGAATAAGACAACTTTAGTGGG
CCAGATGGAGAACAACAATTGTAATGAACTAAATAAAAGCAAAATCATTGTTAAAAAGAAACCGAAGCAACTAAATCCAT
TTCATCTGAAAGTGGGTAATGAAGTGTTAAGGCAGAGGAAAAACTGGTGGAAGGACAGTCGCTTCCGGTCTGAATGGGTC
AGCCCTTGTGTCATAGACTACATTATGGAGAACGGGGGCACTGTTCTTCGAGACAGCTCTGGGGCTAGACTTAAACGACC
TATCAAGATGTCCCACCTGAAGCCCTATGTCAGAGAATCGGGTGAACAAGATAGTCTCCATCTCTTACACGGTTCAGTAG
TGGCAGATCATGACTATGTTGGAATGCCCGAGCTGCCAGTTGGAGCATACCAAGCAAGTATTCTGGTGGAACATGCGGCT
ATTGGAGTAGACGACAGTGAGTTACTGACGTCAAGCAAGGATCGTGAACTATTAGAATACAGAAATGCCAAAATCTCTCC
ATTGATGGAAGATCATAATGCTCTTGAAAAGCAGACTTTTAGTCTCTTGGACTCTTCAAACCAAGTCCTTGAGTACTTAA
CT

Alignment

ORF - retro_btau_598 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.26 %
• Parental protein coverage: 90.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEKKKVLRECHENDTGAHHGISRTLTLVESSYYWTSVTNDVKQWVYACQHCQVAKNTVILAPKQHLLKVE
          .EK.KVLRECHENDTGAHHGISRTLTLVESSYYWTSVTNDVKQWVYACQHCQVAKNTVILAPKQHLLKVE
Retrocopy EEKNKVLRECHENDTGAHHGISRTLTLVESSYYWTSVTNDVKQWVYACQHCQVAKNTVILAPKQHLLKVE

Parental  NPWSIVTVDLMGPFHTSNRSHVYAIIMTDLFTKWVVILPLCDVSASEISKAIINIFFLYGPPQKIIMDQR
          NPWSIVTVDLMGPFHTSNRSHVYAIIMTDLFTKWVVILPL.DVSASEISKA.INIFFLYGPPQKIIMDQR
Retrocopy NPWSIVTVDLMGPFHTSNRSHVYAIIMTDLFTKWVVILPLWDVSASEISKASINIFFLYGPPQKIIMDQR

Parental  DEFIHQINVELCELFGTKQIVISHASQTINPAESTPSTIKTFLSKHCVDYPNDWDDHLPAVSFAFNVTHL
          DEFIHQINVELCELFGTKQIVISHASQTINPAESTPSTIKTFLSKHC.DYPNDWDDHLPAVSFAFNVTH.
Retrocopy DEFIHQINVELCELFGTKQIVISHASQTINPAESTPSTIKTFLSKHCADYPNDWDDHLPAVSFAFNVTHF

Parental  EPTKNTPYFQMFNRNPYMPESSDIREVDGDNTSMFAKILDAIKEADKIMENKTTSVGQMENNNCHELNKS
          EPTKNTPYFQMFNRN.YMPESSDI.EVDGDNTSMFAKILDAIKEADKIMENKTT.VGQMENNNC.ELNKS
Retrocopy EPTKNTPYFQMFNRNLYMPESSDIHEVDGDNTSMFAKILDAIKEADKIMENKTTLVGQMENNNCNELNKS

Parental  KIIVKKKPKQQNPFHLKVGHEVLRQRKNWWKDGRFRSEWVGPCVIDYITENGGAVLRDSSGARLKRPIKM
          KIIVKKKPKQ.NPFHLKVG.EVLRQRKNWWKD.RFRSEWV.PCVIDYI.ENGG.VLRDSSGARLKRPIKM
Retrocopy KIIVKKKPKQLNPFHLKVGNEVLRQRKNWWKDSRFRSEWVSPCVIDYIMENGGTVLRDSSGARLKRPIKM

Parental  SHLKPYVRESGEQDSLHLLHGSVVADHDYVGMPELPVGAYQASILVEDAAIGVDDSELLTSSKDRELLEY
          SHLKPYVRESGEQDSLHLLHGSVVADHDYVGMPELPVGAYQASILVE.AAIGVDDSELLTSSKDRELLEY
Retrocopy SHLKPYVRESGEQDSLHLLHGSVVADHDYVGMPELPVGAYQASILVEHAAIGVDDSELLTSSKDRELLEY

Parental  RNAKISPLMEDHNALEKQTFSLLDSSNQVLEYLT
          RNAKISPLMEDHNALEKQTFSLLDSSNQVLEYLT
Retrocopy RNAKISPLMEDHNALEKQTFSLLDSSNQVLEYLT

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	0.14 RPM	6.49 RPM
ERP005899_muscle	0.00 RPM	2.16 RPM
SRP017611_brain	0.00 RPM	3.43 RPM
SRP017611_kidney	0.12 RPM	5.28 RPM
SRP017611_liver	0.00 RPM	3.78 RPM
SRP030211_testis	0.10 RPM	38.12 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_598 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_598 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_598 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	ENSBTAG00000021471	1 retrocopy	retro_btau_598 ,
Otolemur garnettii	ENSOGAG00000008147	1 retrocopy	retro_ogar_1377,