RetrogeneDB ID: retro_btau_1748

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:72584543..72585195(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM168A
• Ensembl ID: ENSBTAG00000016497
• Aliases: None
• Description: protein FAM168A [Source:RefSeq peptide;Acc:NP_001192501]

Sequence

>retro_btau_1748
GCTTATACAAGTTATCCCACAGCCTATCCAATTGCAGCCCCTGCTTACAATCCCAGCCTGTACCCTGCCACTAGCTCCCC
TTATGCTCCAGCAACTCTGCTGATGAAATAGACCTGGCTAGAGAACTCATCTTCCTGTGCCACTGAAGGTACCTATTTCT
ACCTCCCAGTGGACACCAGGACCGAGAGCCAAACTTACCAAACATCCTCTGCAGCTTTCAGATATACAGAGGGGACACCA
TACAAGGTCCCACCAGCCCAGAGTAATACTGCCCTGATCCCCCTACTCCTCTTCACCCAATCCCTATCAGATGGTCATGC
ATCCAATCATAAGTGCCTACCCCTAGCAGAATCTGTATGTCCTGGGAGCCTAGGACACAAAGCTGGTGTATGCTGCCCAG
GCTTATGTCATCCACTACACCATGGTCATCCAGCCTAACAGTACTCACTCTGCCATCTACCAGACACCAGTAAACCCTCC
CAATACCAATGTCATGGCCATGGGCATGGTGGCTGGCACCACCGTGATGATGTCAACATGTACCCTGCTGACTGCATCAC
AGCACACAGCGATTGGGGCATACCCTGTCTTCATGCCAACATACAGGGCACAAGGGATCCTTGCATACAGCTATATATAT
GCCCCACACTGG

Alignment

ORF - retro_btau_1748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.57 %
• Parental protein coverage: 97.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AYPAAAPAYNPSLYPTNSPSYAPEFQFLHSAYATLLMKQAWPQNSSSCGTEGT-FHLPVDTGTENRTYQA
          AY.....AY.P...P...PS..P.......A.ATLLMK..W..NSSSC.TEGT.F.LPVDT.TE..TYQ.
Retrocopy AYTSYPTAY-PIAAPAYNPSLYPATSSPY-APATLLMK*TWLENSSSCATEGTYFYLPVDTRTESQTYQT

Parental  SSAAFRYTAGTPYKVPPTQSNTAP-PPYSPSPNPYQTAMYPIRSAYPQQNLYAQGAYYTQPVYAAQPHVI
          SSAAFRYT.GTPYKVPP.QSNTA...PYS.SPNPYQ..M.PI.SAYP.QNLY..GA..T..VYAAQ..VI
Retrocopy SSAAFRYTEGTPYKVPPAQSNTAL>SPYSSSPNPYQMVMHPIISAYP*QNLYVLGA*DTKLVYAAQAYVI

Parental  HHTTVVQPNSIPSAIYPAPVAAPRTNGVAMGMVAGTTMAMSAGCSGTLLTAPQHTAIGAHPVSMPTYRAQ
          H.T.V.QPNS..SAIY..PV..P.TN..AMGMVAGTT..MS.....TLLTA.QHTAIGA.PV.MPTYRAQ
Retrocopy HYTMVIQPNSTHSAIYQTPVNPPNTNVMAMGMVAGTTVMMS---TCTLLTASQHTAIGAYPVFMPTYRAQ

Parental  GTPAYSYV-PPHW
          G..AYSY...PHW
Retrocopy GILAYSYIYAPHW

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	0.65 RPM
ERP005899_muscle	0.00 RPM	4.75 RPM
SRP017611_brain	0.00 RPM	19.19 RPM
SRP017611_kidney	0.00 RPM	8.42 RPM
SRP017611_liver	0.00 RPM	2.72 RPM
SRP030211_testis	0.00 RPM	2.55 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1748 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1748 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	ENSBTAG00000016497	1 retrocopy	retro_btau_1748 ,
Ictidomys tridecemlineatus	ENSSTOG00000014507	1 retrocopy	retro_itri_1722,