RetrogeneDB ID: retro_mmus_781

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:33427884..33428406(-)
• Located in intron of: ENSMUSG00000040594

Retrocopy information

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

Parental gene information

• Parental gene symbol: Med29
• Ensembl ID: ENSMUSG00000003444
• Aliases: None
• Description: mediator complex subunit 29 [Source:MGI Symbol;Acc:MGI:1914474]

Sequence

>retro_mmus_781
CCGGGTCCCCAGCAACAGCCGCAACCGACCCAGTTGGTGGGTTCTGCCCAGAGCGGGCTCCTGCAGCAGCAGCAGCAGGA
CTTCGATCCTGTGCAGCGCTACAAGATGCTCATCCCGCAACTGAAGGAGAGTCTCCAGACTTTGATGAAGGTTGCAGCCC
AGAATCTGATTCAGAACACTAACATTGACAACGGACAGAAGAGCAGTGACACACCCTTGCAGCACTTTGACAAGTGTTTG
GAGGAGTTTTACGCACTCTGTGATCAGCTGGAACTCTGCTTGCGCCTGGCCCACGAGTGCCTTTCACAGAGCTGTGACAG
CGCCAAACACTCTCCAACACTGGTACCCACAGCCACAAAGCCAGATGCAGTGCAGCCAGACAGTCTGCCCTACCCACAGT
ACCTGGCTGTCATCAAAGCCCAGATCACCTGTGCCAAAGACATTCATACTGCCCTGCTGGACTGTGCCAACAAGGTCACT
GGAAAGACTACTGCACCCTCTACTGGCCCTGGGGGCAGCCTC

Alignment

ORF - retro_mmus_781 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.85 %
• Parental protein coverage: 87.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGPQQQPQPTQLVGSAQSGLLQQQQQDFDPVQRYKMLIPQLKESLQTLMKVAAQNLIQNTNIDNGQKSSD
          PGPQQQPQPTQLVGSAQSGLLQQQQQDFDPVQRYKMLIPQLKESLQTLMKVAAQNLIQNTNIDNGQKSSD
Retrocopy PGPQQQPQPTQLVGSAQSGLLQQQQQDFDPVQRYKMLIPQLKESLQTLMKVAAQNLIQNTNIDNGQKSSD

Parental  APLQRFDKCLEEFYALCDQLELCLRLAHECLSQSCDSAKHSPTLVPTATKPDAVQPDSLPYPQYLAVIKA
          .PLQ.FDKCLEEFYALCDQLELCLRLAHECLSQSCDSAKHSPTLVPTATKPDAVQPDSLPYPQYLAVIKA
Retrocopy TPLQHFDKCLEEFYALCDQLELCLRLAHECLSQSCDSAKHSPTLVPTATKPDAVQPDSLPYPQYLAVIKA

Parental  QITCAKDIHTALLDCANKVTGKTTAPSTGPGGSL
          QITCAKDIHTALLDCANKVTGKTTAPSTGPGGSL
Retrocopy QITCAKDIHTALLDCANKVTGKTTAPSTGPGGSL

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
SRP007412_brain	0.02 RPM	5.00 RPM
SRP007412_cerebellum	0.09 RPM	4.47 RPM
SRP007412_heart	0.06 RPM	4.26 RPM
SRP007412_kidney	0.02 RPM	6.66 RPM
SRP007412_liver	0.00 RPM	3.63 RPM
SRP007412_testis	0.09 RPM	12.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_781 was not detected

EST

No EST(s) were mapped for retro_mmus_781 retrocopy.

TSS

No TSS is located nearby retro_mmus_781 retrocopy 5' end.

Lab

retro_mmus_781 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_781 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
Echinops telfairi	ENSETEG00000000406	1 retrocopy	retro_etel_1524,
Mus musculus	ENSMUSG00000003444	1 retrocopy	retro_mmus_781 ,