RetrogeneDB ID: retro_mmus_1538

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:3056686..3057121(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000044697
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Synj2bp
• Ensembl ID: ENSMUSG00000090935
• Aliases: None
• Description: synaptojanin 2 binding protein [Source:MGI Symbol;Acc:MGI:1344347]

Sequence

>retro_mmus_1538
ATGAACAAATGGGTGGATTATTCAGTCATGGAGGAAGAGATCAACCTGATGAGAGGACCCTCGGGGCTGGGCTTCAACAA
TGTCGGTGAGACAGATCAACAGTATGTGTCCAAGGACAGTGGCATCTATGACAGCCGCATCAAAGAGGATGGGGCTGTGG
CCCAGGATGGGCGGCTCCAGGAGGGTGACAAGATCCTCTCAGTAAATGACCAAGATCTGAAGAACCTGCTGCACCAAGAT
GCTGTAGACCTCTTCCGTAATGCGGGATGTGCTGTGTCCCTGAGAGTACAGCACAGGTTACCAGTGCAGAACGGACCTAT
AGTACATCGAGGTGAAGGAGAGCCAAGTGGAGTTCCTGTAGCTATGGTGCTGCTACCAGTGTTTGCCCTCACCACGGTAG
CAGTTTGGGCCTTCGTGGGATACTGAAAGCAGCTT

Alignment

ORF - retro_mmus_1538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGRVDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKEDGAAAQDGRLQEGDKILSVNG
          MN..VDY.V.EEEINL.RGPSGLGFN.VG.TDQQYVS.DSGIY.SRIKEDGA.AQDGRLQEGDKILSVN.
Retrocopy MNKWVDYSVMEEEINLMRGPSGLGFNNVGETDQQYVSKDSGIYDSRIKEDGAVAQDGRLQEGDKILSVND

Parental  QDLKNLLHQDAVDLFRNAGCAVSLRVQHRLPVQNGPIVHRGEGEPSGVPVAMVLLPVFALTMVAVWAFVR
          QDLKNLLHQDAVDLFRNAGCAVSLRVQHRLPVQNGPIVHRGEGEPSGVPVAMVLLPVFALT.VAVWAFV.
Retrocopy QDLKNLLHQDAVDLFRNAGCAVSLRVQHRLPVQNGPIVHRGEGEPSGVPVAMVLLPVFALTTVAVWAFVG

Parental  YRKQL
          Y.KQL
Retrocopy Y*KQL

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	0.00 RPM	30.56 RPM
SRP007412_cerebellum	0.00 RPM	31.48 RPM
SRP007412_heart	0.03 RPM	34.93 RPM
SRP007412_kidney	0.04 RPM	42.91 RPM
SRP007412_liver	0.00 RPM	43.61 RPM
SRP007412_testis	0.41 RPM	29.09 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1538 was not detected

EST

No EST(s) were mapped for retro_mmus_1538 retrocopy.

TSS

No TSS is located nearby retro_mmus_1538 retrocopy 5' end.

Lab

retro_mmus_1538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1538 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	ENSBTAG00000007586	1 retrocopy	retro_btau_1114,
Cavia porcellus	ENSCPOG00000023967	1 retrocopy	retro_cpor_836,
Dipodomys ordii	ENSDORG00000010450	1 retrocopy	retro_dord_443,
Gorilla gorilla	ENSGGOG00000014492	1 retrocopy	retro_ggor_1470,
Macaca mulatta	ENSMMUG00000011086	1 retrocopy	retro_mmul_2308,
Mus musculus	ENSMUSG00000090935	3 retrocopies	retro_mmus_1428, retro_mmus_1538 , retro_mmus_1802,
Oryctolagus cuniculus	ENSOCUG00000008559	1 retrocopy	retro_ocun_885,
Otolemur garnettii	ENSOGAG00000013211	1 retrocopy	retro_ogar_1515,