RetrogeneDB ID: retro_btau_1767

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:111704129..111704833(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.91730
• Ensembl ID: ENSBTAG00000010357
• Aliases: ST6GAL1, SIAT1
• Description: beta-galactoside alpha-2,6-sialyltransferase 1 [Source:RefSeq peptide;Acc:NP_803483]

Sequence

>retro_btau_1767
CTCAGGAGGACATTAGGACCAAGGCAGTGGGGCAGGTGTGTCTCTCCAGCAGGATCTCTGAAGTCCTCCCGGCTAGGTCG
AGAAATAGATGATCATGATGCAGTCCAGAGGTTTAATGGGGCACCCACAGTCAAATTCCAACAAGACGTGGGCACGAAAA
CCACCATTCGTCTGGTAAACTCTCAGTTGGTCACCACAGAAGCGGGCTTCCTGAAAGACAGTTTGTACAATGAAGGAATC
CTAATTGTGTGGGACCCATCTGTTTACCATTCAGATATCCCAAAGTGGTACAGGAATCCCGACTACAGTTTCTTCAATAA
CTTCAAGAGCTATCGTAAGCTGCATCCTGATCAGCCCTTTTACATCCTCAAGTCCCAGATGCCTTGGGAGCTGTGGGACA
TCATTCAAGAAATCTCCTCAGAGCAGATCCAGCCAAACCCCCTGTCCTCCGGATGCTCGGCATTGTCATTATGATGTTAC
TGTGTGACCAAGTGGTTATTTACAAGTTCCTCTCATCCAAGCGCAAGACTGATGTATGCAACTACTATCAGAGGTATTTT
GACAGTGCCTGCACAATGGGCGCCTAACACCCACTCCTCTTTGAGAAGAACATGGTGAAGCGCCTCAACCTCGGCACAGA
CAAGGACATCTACCTGCTCGGAAAAGCCACGCTGCATGGCTTCCGGACAATTCGCTGTGGAGCA

Alignment

ORF - retro_btau_1767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 58.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRTKAGP--WGRCAVVSSAGSLKSSRLGREIDDHDAVLRFNGAPTVKFQQDVGTKTTIRLVNSQLVTTEA
          .R...GP..WGRC..VS.AGSLKSSRLGREIDDHDAV.RFNGAPTVKFQQDVGTKTTIRLVNSQLVTTEA
Retrocopy LRRTLGPRQWGRC--VSPAGSLKSSRLGREIDDHDAVQRFNGAPTVKFQQDVGTKTTIRLVNSQLVTTEA

Parental  GFLKDSLYNEGILIVWDPSVYHSDIPKWYRNPDYSFFNNFKSYRKLHPDQPFYILKPQMPWELWDIIQEI
          GFLKDSLYNEGILIVWDPSVYHSDIPKWYRNPDYSFFNNFKSYRKLHPDQPFYILK.QMPWELWDIIQEI
Retrocopy GFLKDSLYNEGILIVWDPSVYHSDIPKWYRNPDYSFFNNFKSYRKLHPDQPFYILKSQMPWELWDIIQEI

Parental  SSELIQPNPPSSG-MLGIAIMMSLCDQVDIYEFLPSKRKTDVCYYYQRYFDSACTMGAYHPLLFEKNMVK
          SSE.IQPNP.SSG.MLGI.IMM.LCDQV.IY.FL.SKRKTDVC.YYQRYFDSACTMGA.HPLLFEKNMVK
Retrocopy SSEQIQPNPLSSG<MLGIVIMMLLCDQVVIYKFLSSKRKTDVCNYYQRYFDSACTMGA*HPLLFEKNMVK

Parental  YLNLGTDEDIYLLGKATLPGFRTIRCGA
          .LNLGTD.DIYLLGKATL.GFRTIRCGA
Retrocopy RLNLGTDKDIYLLGKATLHGFRTIRCGA

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	23.79 RPM
ERP005899_muscle	0.00 RPM	17.58 RPM
SRP017611_brain	0.00 RPM	5.89 RPM
SRP017611_kidney	0.00 RPM	13.93 RPM
SRP017611_liver	0.83 RPM	359.95 RPM
SRP030211_testis	0.02 RPM	9.57 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1767 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1767 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1767 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010357	1 retrocopy	retro_btau_1767 ,
Bos taurus	ENSBTAG00000044129	1 retrocopy	retro_btau_987,
Canis familiaris	ENSCAFG00000013698	1 retrocopy	retro_cfam_2158,
Felis catus	ENSFCAG00000013886	1 retrocopy	retro_fcat_1983,
Macaca mulatta	ENSMMUG00000014905	1 retrocopy	retro_mmul_630,
Nomascus leucogenys	ENSNLEG00000006676	1 retrocopy	retro_nleu_2774,
Pongo abelii	ENSPPYG00000014388	1 retrocopy	retro_pabe_3575,