RetrogeneDB ID: retro_btau_27

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:23792292..23793276(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046593
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FTSJ1
• Ensembl ID: ENSBTAG00000031829
• Aliases: None
• Description: putative ribosomal RNA methyltransferase 1 [Source:RefSeq peptide;Acc:NP_001071402]

Sequence

>retro_btau_27
ATGGGATGGTCATCAAAGGACAAGCGAGATGTCTACTACCGGCTAGCCAAGGAGAAAGGCTGGCGCGCTCGTAGTGCCTT
CAAGCTGTTACAACTTGACGAGGAATTCCAGCTCTTCCAAGGCGTGACGCGGGCGATTGACCTGTGTGCGGCCCCAGGCA
GCTGGAGCCAAGTGCTGAGCCAGAAGATAGGGGGCCAGGGTTCTGGCCATGTGGTGGCTGTGGACCTTCAGGCAATGGCT
CCACTACCAGGTGTGTTACAGATCCAGGGGGATATCACCCAGCTGTCCACTGCCAAGGAGATCATCCAGCACTTTGAAGA
CTGCCCCACGGACCTAGTGGTGTGTGACGGGGCTCCTGATGTAACCGGCCTCCATGTTGAGTATATGCAGGCCCAGCTCC
TCCTAGCTGCTCTGAACCTTGCCATGCACGTCTTGAAGCCAGGGGGCTGCTTTGTGGGCAAGATCTTCCGAGGCCGGGAT
GTGACACTGATCTACAGCCAGCTGCGTGTCTTCTTCTCCAGGGTGCTATGTGCCAAGCCCAGGAGCAGCCGAAATTCCAG
CATCGAGGCCTTTGCTGTCTGTAAGGGTTACAACCCTCCTGAGGGCTTCCTGCCCGACTTGACCAAACCCTTGCTGGATC
ACTCTTACGATTTCAACCAATTGGATGGCCTCAGCCGCATCATTGTGCCATTTGTGACCTCTGGGGACCTGAGCGCCTAT
GATTCAGACTGCAGTTACCCACTGGACCTAGAGGACGGCTCAGAATACAAGTGCACTCCACCCAGGCAGCCCCCCATCTC
ACCACCCTACCAGGAGGCGAGCACATTGAAGGAGAAAGGGCAGCTGGCCAAGGACAAGGAGATCCGCCCTCAGGACTGCC
CCACGAGCACAGTGGACAGGATGCCCCAGTCCCTGACTGTTCCACAGCGCCACACCCTGCAGCCCTCTGAGGTCGAAGAC
AGTGGAGTGAATTATTCGTCTTAA

Alignment

ORF - retro_btau_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 82.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRTSKDKRDVYYRLAKENGWRARSAFKLLQLDEEFQLFQGVTRAVDLCAAPGSWSQVLSQKIGGQGSGH
          MG..SKDKRDVYYRLAKE.GWRARSAFKLLQLDEEFQLFQGVTRA.DLCAAPGSWSQVLSQKIGGQGSGH
Retrocopy MGWSSKDKRDVYYRLAKEKGWRARSAFKLLQLDEEFQLFQGVTRAIDLCAAPGSWSQVLSQKIGGQGSGH

Parental  VVAVDLQAMAPLPGVLQIQGDITQLSTAKEIIQHFEGCPADLVVCDGAPDVTGLHDVDEYMQAQLLLAAL
          VVAVDLQAMAPLPGVLQIQGDITQLSTAKEIIQHFE.CP.DLVVCDGAPDVTGLH...EYMQAQLLLAAL
Retrocopy VVAVDLQAMAPLPGVLQIQGDITQLSTAKEIIQHFEDCPTDLVVCDGAPDVTGLH--VEYMQAQLLLAAL

Parental  NIATHVLKPGGCFVAKIFRGRDVTLIYSQLRVFFSSVLCAKPRSSRNSSIEAFAVCKGYDPPEGFLPDLT
          N.A.HVLKPGGCFV.KIFRGRDVTLIYSQLRVFFS.VLCAKPRSSRNSSIEAFAVCKGY.PPEGFLPDLT
Retrocopy NLAMHVLKPGGCFVGKIFRGRDVTLIYSQLRVFFSRVLCAKPRSSRNSSIEAFAVCKGYNPPEGFLPDLT

Parental  KPLLDHSYDPDFNQLDGPTRIIVPFVTCGDLSAYDSDRSYPLD
          KPLLDHSY..DFNQLDG..RIIVPFVT.GDLSAYDSD.SYPLD
Retrocopy KPLLDHSY--DFNQLDGLSRIIVPFVTSGDLSAYDSDCSYPLD

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	20.40 RPM
ERP005899_muscle	0.00 RPM	13.67 RPM
SRP017611_brain	0.14 RPM	15.71 RPM
SRP017611_kidney	0.00 RPM	27.03 RPM
SRP017611_liver	0.00 RPM	21.60 RPM
SRP030211_testis	17.29 RPM	8.09 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_27 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_27 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_27 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031829	1 retrocopy	retro_btau_27 ,
Canis familiaris	ENSCAFG00000015339	1 retrocopy	retro_cfam_544,
Erinaceus europaeus	ENSEEUG00000001469	1 retrocopy	retro_eeur_222,
Echinops telfairi	ENSETEG00000014092	3 retrocopies	retro_etel_1697, retro_etel_1803, retro_etel_1928,
Myotis lucifugus	ENSMLUG00000003977	1 retrocopy	retro_mluc_1329,
Oryctolagus cuniculus	ENSOCUG00000008009	1 retrocopy	retro_ocun_870,
Otolemur garnettii	ENSOGAG00000016174	1 retrocopy	retro_ogar_180,
Sorex araneus	ENSSARG00000007091	1 retrocopy	retro_sara_26,