RetrogeneDB ID: retro_btau_306

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:96220623..96221277(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPV17L2
• Ensembl ID: ENSBTAG00000025788
• Aliases: None
• Description: Mpv17-like protein 2 [Source:UniProtKB/Swiss-Prot;Acc:A5D787]

Sequence

>retro_btau_306
ATGCCGCCCGGCGGCTGGCGCTGGCTGCGCGGCCTTTGGGCTGCGGGTCAGCCCCTGTTCCAAGGCCGTGCGTTGCTCGT
CACCAACACCCTGGGATGCGGCGTTCTCATGGCGGCTGGGGATGGGGCGTGCCAGACCTGGGAGATTCACGCCCGGCCCG
GCCAGAAGTTCGACCCGCGGCGCTCAGTGAGCATGTTTGCAGTCGGCTGCAGCATGGGCCCCTTCCTGCACTATTGGTAT
CTCTGGCTGGACCGCCTGTTCCCTGCATCTGGCTTCCCTGGCCTCCCAAACGTCCTCAAGAAGGTCCTCATTGACCAACT
GGTGGCCTCTCCTATGCTTGGCGTCTGGTACTTCTTGGGCCTTGGCTGCCTGGAGGGCCAGACCCTGGACAAGAGCTGTC
AGGAGCTGCGGGACAAGTTCTGGGAATTCTACAAGGCTGACTGGTGTGTGTGGCCTGCTGCGCAGCTGGTGAATTTCCTC
TTCGTGCCCCCCCAGTTCTGAATCACCTACATCAGCGGCCTGACGCTAGGGTGGGACACCTACCTCTCCTACCTGAAATA
CCGGATCCCAGGCCCTCTGACACCCCCAGGCTGTGTGGCCCTGGGCACCATACAGACTGAGCCCCCAGATGCCAGACAGC
AAGGCAAGACTGAC

Alignment

ORF - retro_btau_306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPGGWRWLRGLWAAGQPLFQGRALLVTNTLGCGVLMAAGDGARQTWEIRARPGQKFDPRRSVSMFAVGC
          MPPGGWRWLRGLWAAGQPLFQGRALLVTNTLGCGVLMAAGDGA.QTWEI.ARPGQKFDPRRSVSMFAVGC
Retrocopy MPPGGWRWLRGLWAAGQPLFQGRALLVTNTLGCGVLMAAGDGACQTWEIHARPGQKFDPRRSVSMFAVGC

Parental  SMGPFLHYWYLWLDRLFPASGFPGLPNVLKKVLIDQLVASPMLGVWYFLGLGCLEGQTLDKSCQELRDKF
          SMGPFLHYWYLWLDRLFPASGFPGLPNVLKKVLIDQLVASPMLGVWYFLGLGCLEGQTLDKSCQELRDKF
Retrocopy SMGPFLHYWYLWLDRLFPASGFPGLPNVLKKVLIDQLVASPMLGVWYFLGLGCLEGQTLDKSCQELRDKF

Parental  WEFYKADWCVWPAAQLVNFLFVPPQFRVTYINGLTLGWDTYLSYLKYRIPGPLTPPGCVALGTIQTEPPD
          WEFYKADWCVWPAAQLVNFLFVPPQF..TYI.GLTLGWDTYLSYLKYRIPGPLTPPGCVALGTIQTEPPD
Retrocopy WEFYKADWCVWPAAQLVNFLFVPPQF*ITYISGLTLGWDTYLSYLKYRIPGPLTPPGCVALGTIQTEPPD

Parental  ARQQGKTD
          ARQQGKTD
Retrocopy ARQQGKTD

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	0.07 RPM	1.59 RPM
ERP005899_muscle	0.21 RPM	25.34 RPM
SRP017611_brain	0.05 RPM	4.98 RPM
SRP017611_kidney	0.06 RPM	10.25 RPM
SRP017611_liver	0.23 RPM	10.95 RPM
SRP030211_testis	0.06 RPM	4.35 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_306 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_306 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000027644	1 retrocopy	retro_acar_180,
Bos taurus	ENSBTAG00000025788	1 retrocopy	retro_btau_306 ,
Callithrix jacchus	ENSCJAG00000014104	1 retrocopy	retro_cjac_4063,
Echinops telfairi	ENSETEG00000013840	1 retrocopy	retro_etel_1446,
Macropus eugenii	ENSMEUG00000016379	2 retrocopies	retro_meug_223, retro_meug_943,
Macaca mulatta	ENSMMUG00000005025	1 retrocopy	retro_mmul_2493,
Nomascus leucogenys	ENSNLEG00000005944	1 retrocopy	retro_nleu_2666,
Pteropus vampyrus	ENSPVAG00000002028	1 retrocopy	retro_pvam_1254,