RetrogeneDB ID: retro_btau_1792

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:4734784..4735501(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM219
• Ensembl ID: ENSBTAG00000021785
• Aliases: TMEM219, IGFBP-3R
• Description: Transmembrane protein 219 [Source:UniProtKB/Swiss-Prot;Acc:Q1JQE1]

Sequence

>retro_btau_1792
ATGGGCATCTGCCAGGCAGGGCACTACCTGCATCTCTTCCTGGCCCACCACCCACCTCTGGTCTGTGCCACTTTGATCCT
GCTGCTTCTTGGCCTTTCTGGCCTGGGTCTTGGTGGCTTCCTCCTCACCCACAGAACTGACCTGCACAGCCCTGACATCT
CCCAGGACTGGGTCTCCTTCTTGAGATCTTTTGGCCAGCTGGCCCTGTGCCCGGTGAATGGGACAGTCACAAGGAAGGGG
CGTGGGTCTCATGTCGTGGGCTTACTGGCCACCTTGAACTTTGGAGATGGTCCAGACAGGAACAAGACCCAGACATTCCA
AGCCCAGGTCCAGGGTAGCCCGATGGGATTGAAAGGATCTTTTGCAGGAAAGCTGGTGCTCGTTACGGCCAGGGTGACCA
CAGAAAGGACCCCAGGAATCTGCCTGTAGTTTAGTGCTACTCCAGAAATCCTGCCCTCCAGCCAGCCACCGATACCCTGC
TCAGAGGAGGGAGCAAGAAATGCCACCCTGAGCCCTAGAATGGCTGAGGAGTGTGTCAGTGTCTGGAGCCACAAAGGTCT
CGTGCTCATCAAGTTGCTCACCTCGGAGGAGCTGATTCTGTGTGGCTCTCGGCTGCTGGCTTTGGGCTTCTCCCTGATTC
TGTTCTGTGGCCTCTGCTGTCTCACTGCAGCGTGCTTCCATCCGCGCCGGGAGTCCCACTGGTCTAGAACTCAGCTC

Alignment

ORF - retro_btau_1792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGSCQAGHYLHFCLAHHPPLVCATLILLLLGLSGLGLGGFLLTHRTDLRSPDIPQDWVSFLRSFGQLTLC
          MG.CQAGHYLH..LAHHPPLVCATLILLLLGLSGLGLGGFLLTHRTDL.SPDI.QDWVSFLRSFGQL.LC
Retrocopy MGICQAGHYLHLFLAHHPPLVCATLILLLLGLSGLGLGGFLLTHRTDLHSPDISQDWVSFLRSFGQLALC

Parental  PVNGTVTGKGRGSHIVGLLTTLNFGDGPDRNKTQTFQAQVQGSRMGLKGSFARELVLVTARVTTERTPGT
          PVNGTVT.KGRGSH.VGLL.TLNFGDGPDRNKTQTFQAQVQGS.MGLKGSFA..LVLVTARVTTERTPG.
Retrocopy PVNGTVTRKGRGSHVVGLLATLNFGDGPDRNKTQTFQAQVQGSPMGLKGSFAGKLVLVTARVTTERTPGI

Parental  CLYFSAIPEILPSSQPPIPCSEEGAGNATLSPRMSEECVGVWSHEGLVLTKLLTSEELTLCGSRLLVLGF
          CL.FSA.PEILPSSQPPIPCSEEGA.NATLSPRM.EECV.VWSH.GLVL.KLLTSEEL.LCGSRLL.LGF
Retrocopy CL*FSATPEILPSSQPPIPCSEEGARNATLSPRMAEECVSVWSHKGLVLIKLLTSEELILCGSRLLALGF

Parental  FLILFCGLCCLTAACFHPRRESHWSRTRL
          .LILFCGLCCLTAACFHPRRESHWSRT.L
Retrocopy SLILFCGLCCLTAACFHPRRESHWSRTQL

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	0.14 RPM	8.44 RPM
ERP005899_muscle	0.00 RPM	32.73 RPM
SRP017611_brain	0.00 RPM	13.66 RPM
SRP017611_kidney	0.00 RPM	33.19 RPM
SRP017611_liver	0.53 RPM	19.78 RPM
SRP030211_testis	0.02 RPM	27.88 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1792 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1792 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1792 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021785	1 retrocopy	retro_btau_1792 ,
Microcebus murinus	ENSMICG00000009088	1 retrocopy	retro_mmur_610,
Macaca mulatta	ENSMMUG00000020273	1 retrocopy	retro_mmul_2266,
Oryctolagus cuniculus	ENSOCUG00000006318	1 retrocopy	retro_ocun_517,