RetrogeneDB ID: retro_btau_796

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:36046534..36047174(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKA3
• Ensembl ID: ENSBTAG00000003314
• Aliases: SKA3, C12H13ORF3
• Description: Spindle and kinetochore-associated protein 3 [Source:UniProtKB/Swiss-Prot;Acc:A8PUI7]

Sequence

>retro_btau_796
ATGGATCCAATCTGAGGCTTTTGCAGGATGCTGAGGTCTCTGGCTATCACCCTGGATGGCAAGACGGCCCAGCTGTAGTG
AGTGCTGGACAGAGAGGAAAGCAACTCTGAAGATTGTCCAATGAGAGTTTTACATGACCTTCACTCAGAAGTACAGACTC
TAAAGGATGATGTCAATATTCTTGATAAAGCAAAGCTTGGAAAGTCGAGAAAGCATTGGTTTCATAAAGGCAACAAAAAT
ACTGATGAAAAAGAATTCAATGGATATCATGAAAATAAAAGAGTTTTTCCAGAAGTATGGATATACTCCATGTGCCAAGA
AAAACTCAGTGGATGAGCAAGAGGTCACTGACTCTAAACCAGCGTCCAGTGAATGTGAACGTCCTGAGAAGCCTGACGTG
GAAGATGATTTGTTGGATTTTGCTGTTCCAAGCACTTCTGTTTCTGAGAAGTCACCACATAGTCCACAACTTTCTGATTT
TGGACTTGAGCAGTACATCGTATCCCAAGTTCTGCCAAACCCTCCCCAAGCAGTAAACAATGAGAAGGAAGAGCCAAAAA
TTTTAACTCCATTTTCCAAACAGTCACTAGTAAAAACTTCAAAATGTGCACTAAAGATGGATCATTTTGAGTTGGTATCT

Alignment

ORF - retro_btau_796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.86 %
• Parental protein coverage: 87.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDPIRGFCGKLRSLAVTLDSETARLQRALDGEDSDFEDCPMRVLHDLNSEVRILKDDVNILLDKA-NLES
          MDPI.GFC..LRSLA.TLD..TA.L...LD.E.S..EDCPMRVLHDL.SEV..LKDDVNIL.DKA..LES
Retrocopy MDPI*GFCRMLRSLAITLDGKTAQL**VLDREESNSEDCPMRVLHDLHSEVQTLKDDVNIL-DKA>SLES

Parental  QENIGFIKATKILMRKNSMDIMKIKEFFQKYGYTPRAKKNSVDEQEVTDSKPESSECERPEKPDLKDDLL
          .E.IGFIKATKILM.KNSMDIMKIKEFFQKYGYTP.AKKNSVDEQEVTDSKP.SSECERPEKPD..DDLL
Retrocopy RESIGFIKATKILMKKNSMDIMKIKEFFQKYGYTPCAKKNSVDEQEVTDSKPASSECERPEKPDVEDDLL

Parental  DSAAASTSVSEKSPRSPQLSDFGLERYIVSQVLPNPPQAVNNQKEEPKILTPFSKHSLLKTPKCALKMDD
          D.A..STSVSEKSP.SPQLSDFGLE.YIVSQVLPNPPQAVNN.KEEPKILTPFSK.SL.KT.KCALKMD.
Retrocopy DFAVPSTSVSEKSPHSPQLSDFGLEQYIVSQVLPNPPQAVNNEKEEPKILTPFSKQSLVKTSKCALKMDH

Parental  FECVT
          FE.V.
Retrocopy FELVS

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	1.44 RPM
ERP005899_muscle	0.00 RPM	5.91 RPM
SRP017611_brain	0.00 RPM	21.24 RPM
SRP017611_kidney	0.00 RPM	1.66 RPM
SRP017611_liver	0.00 RPM	0.45 RPM
SRP030211_testis	0.00 RPM	74.32 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_796 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_796 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003314	1 retrocopy	retro_btau_796 ,
Choloepus hoffmanni	ENSCHOG00000003518	1 retrocopy	retro_chof_1706,
Tursiops truncatus	ENSTTRG00000016915	1 retrocopy	retro_ttru_25,