RetrogeneDB ID: retro_btau_987

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:12647620..12648419(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ST6GALNAC6
• Ensembl ID: ENSBTAG00000044129
• Aliases: ST6GALNAC6, siat7f, st6GalNAc-VI
• Description: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6 [Source:UniProtKB/Swiss-Prot;Acc:Q08E15]

Sequence

>retro_btau_987
CCCCAGGGGAGGTGTGACCCCACACCCCTACCCCCTGGGCCATCTGCAGGATGCCGGCCTCTGCCCCACAGCAGTCACCA
GAGAGAGATGAGTAACAACAAACAGCAGCGGTCAGCAGCGTTCCTGATCCTCTTTGCTCTCATCACCACCCTCATCCTCT
GTAGCCCCAACAGTGCGAGTGAGGCCTCTCATTACAGCTCCCTGCGGGGCCAGATCCGCCAGCTGGTCAACCTCAAGAAG
TAGGGCATCACTGACGGCTACATCCCCATTCTCACCCACAAGACACTGCCCTCCTGGTGCTACCAATGTGATTGTCACCA
GCTCCAGCCACCTGCTAGGAACCAAACTGGGCCCTGAGGTCAAGCAGGCAGAGTGCACAATCTGCATGAACGACACCCCC
ACCACAGGCTACTCAGACCACCTTGTGGGTAACAAGACCACCTTCTGCGTAGGGGCCCATTCCAGTGTATTCCGTGTGCT
GTGGAGACTCTAGGAGTTCATCAACCAGACCTCCGAAACCGTGTTCATCTTCTGGGGTGTTCCAAACAAGACGCAGAAGC
CCCAGGACAGCCTGGTGCACGTCGTCCAGTGGGCAGGCCTGGTGTTCCCCAACATGAACGCTTACGCCATCTCTCTTGGC
TGCATGAGCCAGTCTGATGACCTCTTCCAGAGTGAGACGGGCAAGGACAGGGAAGAGTCCTACTCGTGGCTGAGCACAGG
CTGGTTCACCATGGCGACTGCAGTGGAGTAGTGTGACCACGTGCCCATCTATGGCATGGTGCCCCCGGACTACTGCAGC

Alignment

ORF - retro_btau_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.9 %
• Parental protein coverage: 79.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PLSQCDHTPLP-GPPAGHWPLPLSRRRREMKSNKEQRSAVFVILFALITILILYSSSSANEVFHYGSLRG
          P...CD.TPLP.GP.AG..PLP.S...REM..NK.QRSA.F.ILFALIT.LIL.S..SA.E..HY.SLRG
Retrocopy PQGRCDPTPLPPGPSAGCRPLPHSSHQREMSNNKQQRSAAFLILFALITTLILCSPNSASEASHYSSLRG

Parental  RTRRPVNLRKWSITDGYIPILGNKTLPSRCGQC-VIVTSSSHLLGTKLGPEIERAECTIRMNDAPTTGYS
          ..R..VNL.K..ITDGYIPIL..KTLPS.C.QC.....S.SHLLGTKLGPE...AECTI.MND.PTTGYS
Retrocopy QIRQLVNLKK*GITDGYIPILTHKTLPSWCYQC>IVTSS-SHLLGTKLGPEVKQAECTICMNDTPTTGYS

Parental  AD-VGNKTTFRVVAHSSVFHVLRRPQEFVNRTPETVFIFWGPPNKMQKPQGSLVRVIQRAGLVFPNMEAY
          ...VGNKTTF.V.AHSSVF.VL.R..EF.N.T.ETVFIFWG.PNK.QKPQ.SLV.V.Q.AGLVFPNM.AY
Retrocopy DHLVGNKTTFCVGAHSSVFRVLWRL*EFINQTSETVFIFWGVPNKTQKPQDSLVHVVQWAGLVFPNMNAY

Parental  AISLSRMRQFDDLFRSETGKDREKSHSWLSTGWFTMVIAVELCDHVHVYGMVPPDYCS
          AISL..M.Q.DDLF.SETGKDRE.S.SWLSTGWFTM..AVE.CDHV..YGMVPPDYCS
Retrocopy AISLGCMSQSDDLFQSETGKDREESYSWLSTGWFTMATAVE*CDHVPIYGMVPPDYCS

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	6.85 RPM
ERP005899_muscle	0.00 RPM	11.67 RPM
SRP017611_brain	0.00 RPM	43.30 RPM
SRP017611_kidney	0.00 RPM	8.12 RPM
SRP017611_liver	0.00 RPM	20.76 RPM
SRP030211_testis	0.00 RPM	3.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_987 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_987 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	ENSBTAG00000010357	1 retrocopy	retro_btau_1767,
Bos taurus	ENSBTAG00000044129	1 retrocopy	retro_btau_987 ,