RetrogeneDB ID: retro_mmus_1787

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:64611727..64612348(-)
• Located in intron of: ENSMUSG00000039529

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2af1
• Ensembl ID: ENSMUSG00000061613
• Aliases: U2af1, 2010107D16Rik, 35kDa
• Description: U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1 [Source:MGI Symbol;Acc:MGI:98884]

Sequence

>retro_mmus_1787
CGGTTGCACAATAAACCGACCTTTAGCCAGACCATTGCCCTCTTGAACATTTACCGTAACCCTCAAAACTCTTCCCAGTC
CGCTGACGGTTTGCGCTGTGCTGTGAGCGACGTGGAGATGCAGGAGCACTATGATGAGTTCTTTGAGGAAGTCTTCACTG
AGATGGAAGAGAAGTACGGGGAAGTCGAGGAGATGAACGTCTGCGACAACCTAGGGGACCACCTGGTGGGGAACGTGTAT
GTCAAGTTTCGACGTGAGGAGGATGCAGAGAAAGCCATGATCGACTTGAATAACCGTTGGTTTAATGGACAGCCGATCCA
TGCAGAGCTGTCCCCAGTAACTGACTTCAGGGAAGCCTGCTGCCGCCAGTATGAAATGGGAGAGTGCACAAGAGGGGGCT
TCTGCAACTTCATGCATTTGAAGCCCATCTCAAGAGAGCTACGACGGGAGCTGTATGGGCGCCGGCGCAAGAAGCATAGA
TCCAGGTCCCGATCCAGGGAATGGCGTTCCCGAGCCAGAGACCGTGGGCGCGGTGGTAGAGGTAGAGGTGGAGGTGGAGG
TGGCAGAGGACGGGAGCGTGACAGGAGGCAATCAAGAGACTGGGAGAGATCTGGACGATTC

Alignment

ORF - retro_mmus_1787 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.79 %
• Parental protein coverage: 85.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLHNKPTFSQTIALLNIYRNPQNSSQSADGLRCAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN
          RLHNKPTFSQTIALLNIYRNPQNSSQSADGLRCAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN
Retrocopy RLHNKPTFSQTIALLNIYRNPQNSSQSADGLRCAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN

Parental  LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHL
          LGDHLVGNVYVKFRREEDAEKA.IDLNNRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHL
Retrocopy LGDHLVGNVYVKFRREEDAEKAMIDLNNRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHL

Parental  KPISRELRRELYGRRRKKHRSRSRSRERRSRSRDRGRGGGGGGGGGGGR--ERDRRRSRDRERSGRF
          KPISRELRRELYGRRRKKHRSRSRSRE.RSR.RDRGRG..........R..ERDRR.SRD.ERSGRF
Retrocopy KPISRELRRELYGRRRKKHRSRSRSREWRSRARDRGRGXXXXXXXXXXRGRERDRRQSRDWERSGRF

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	17.66 RPM
SRP007412_cerebellum	0.00 RPM	23.36 RPM
SRP007412_heart	0.06 RPM	14.72 RPM
SRP007412_kidney	0.04 RPM	22.33 RPM
SRP007412_liver	0.08 RPM	18.98 RPM
SRP007412_testis	0.09 RPM	13.86 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1787 was not detected

EST

No EST(s) were mapped for retro_mmus_1787 retrocopy.

TSS

No TSS is located nearby retro_mmus_1787 retrocopy 5' end.

Lab

retro_mmus_1787 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1787 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015558	1 retrocopy	retro_ecab_1081,
Homo sapiens	ENSG00000160201	2 retrocopies	retro_hsap_1478, retro_hsap_790,
Loxodonta africana	ENSLAFG00000011460	1 retrocopy	retro_lafr_1135,
Macaca mulatta	ENSMMUG00000022769	2 retrocopies	retro_mmul_1071, retro_mmul_2126,
Mus musculus	ENSMUSG00000031370	1 retrocopy	retro_mmus_233,
Mus musculus	ENSMUSG00000061613	3 retrocopies	retro_mmus_1602, retro_mmus_1787 , retro_mmus_2955,
Mus musculus	ENSMUSG00000078765	1 retrocopy	retro_mmus_540,
Nomascus leucogenys	ENSNLEG00000014737	1 retrocopy	retro_nleu_2382,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pongo abelii	ENSPPYG00000011463	2 retrocopies	retro_pabe_1227, retro_pabe_703,