RetrogeneDB ID: retro_mmus_403

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:191407660..191407956(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pabpn1
• Ensembl ID: ENSMUSG00000022194
• Aliases: None
• Description: poly(A) binding protein, nuclear 1 [Source:MGI Symbol;Acc:MGI:1859158]

Sequence

>retro_mmus_403
TCTGAGGAGCTAGAATCGATCAAGCAAGCTTGAGTCTGGGAGACAGAGGAAGAGGCTGAGAAGCTAAAGGAGCTACAAAG
CAAGGTAGAGAAGCAGGCGAATATGAGTCCACCCCCAGGCAATGCTGGCCCAGTGATCATGTCTCTTGAGGAGAAGATGG
AGGCTGATGCCTGTTCTATCTATGTTGGCAATGTGAACTATGGTGCAACAGCAGAAGAGCTGGGAGCCCACTAAATGGCT
GTGGTTCAGTCAACTGTGTTACTATACTCTGTGACAAATTTAGTGGCCATCCCAGA

Alignment

ORF - retro_mmus_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.0 %
• Parental protein coverage: 59.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEELEAIK-ARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSLEEKMEADARSIYVGNVDYGAT
          SEELE.IK.A.V.E.EEEAEKLKELQ..VEKQ.NMSPPPGNAGPVIMSLEEKMEADA.SIYVGNV.YGAT
Retrocopy SEELESIKQA*VWETEEEAEKLKELQSKVEKQANMSPPPGNAGPVIMSLEEKMEADACSIYVGNVNYGAT

Parental  AEELEAH-FHGCGSVNRVTILCDKFSGHPK
          AEEL.AH...GCGSVN.VTILCDKFSGHP.
Retrocopy AEELGAH<LNGCGSVNCVTILCDKFSGHPR

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	36.89 RPM
SRP007412_cerebellum	0.00 RPM	36.39 RPM
SRP007412_heart	0.03 RPM	9.87 RPM
SRP007412_kidney	0.00 RPM	20.33 RPM
SRP007412_liver	0.00 RPM	12.07 RPM
SRP007412_testis	0.18 RPM	31.70 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_403 was not detected

EST

No EST(s) were mapped for retro_mmus_403 retrocopy.

TSS

No TSS is located nearby retro_mmus_403 retrocopy 5' end.

Lab

retro_mmus_403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_403 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263, retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030,
Loxodonta africana	ENSLAFG00000031227	2 retrocopies	retro_lafr_1031, retro_lafr_233,
Macaca mulatta	ENSMMUG00000014747	1 retrocopy	retro_mmul_2594,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403 ,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023,
Oryctolagus cuniculus	ENSOCUG00000016174	4 retrocopies	retro_ocun_1185, retro_ocun_1741, retro_ocun_1930, retro_ocun_365,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645, retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339, retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625,