RetrogeneDB ID: retro_btau_1771

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:115769176..115769527(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMTM3
• Ensembl ID: ENSBTAG00000047654
• Aliases: None
• Description: CKLF-like MARVEL transmembrane domain-containing protein 3 [Source:RefSeq peptide;Acc:NP_001092869]

Sequence

>retro_btau_1771
TCTGCCTTCCTCACCACCCTCTTGCTTGGGGTCCCTGCCGGCCCTCGATTTTCTCCTCGCTGCTGCCAGGCTGATGAACA
AGTGGCAGGGCTGGTGCAGACCCGTGTTGGACTTCCTAAGAGACATCACAGCGGCCCGCATCTGTTTCGCCATCTCCATC
ACGCCTGTTTGGAAATAACAGGGATGGGGCTGCCTAAGCGGCCCCGGCGTTGGGTTTTCTTGGCCTTCATGCTGTTTGCT
CTTGACTTCAACCTCATCTTTTTCACCATGGCCAAATTTCTCAAACCAGGGGACGCTGCAGAGATGACCACAGGCGACAA
GGCAGAAATAGAGAATTCTGATGATGACTCT

Alignment

ORF - retro_btau_1771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 85.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SAFLTAPLLEF-LLALCFLFADAMQLNDKWQGLCWPMMDFLRCVTAALIYFAISITAVAK-YPDGASKAA
          SAFLT..LL...L.AL.FL.A.A...N.KWQG.C.P..DFLR..TAA.I.FAISIT.V.K...DGA..AA
Retrocopy SAFLTTLLLGV>LPALDFLLAAARLMN-KWQGWCRPVLDFLRDITAARICFAISITPVWK>NRDGAA*AA

Parental  GVFGFF-ATIVFAIDFYLIFNDVAKFLKQEDSAQETTADKAEEEDSDSDS
          ...GF..A...FA.DF.LIF...AKFLK..D.A..TT.DKAE.E.SD.DS
Retrocopy PALGFL>AFMLFALDFNLIFFTMAKFLKPGDAAEMTTGDKAEIENSDDDS

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	1.37 RPM
ERP005899_muscle	0.00 RPM	6.49 RPM
SRP017611_brain	0.00 RPM	2.51 RPM
SRP017611_kidney	0.06 RPM	7.53 RPM
SRP017611_liver	0.00 RPM	3.93 RPM
SRP030211_testis	0.00 RPM	2.98 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1771 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1771 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016093	3 retrocopies	retro_btau_1574, retro_btau_73, retro_btau_810,
Bos taurus	ENSBTAG00000047654	1 retrocopy	retro_btau_1771 ,
Pteropus vampyrus	ENSPVAG00000013762	1 retrocopy	retro_pvam_579,