RetrogeneDB ID: retro_mmus_573

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:73201733..73202349(+)
• Located in intron of: ENSMUSG00000052613

Retrocopy information

• Ensembl ID: ENSMUSG00000091825
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hnrnpa2b1
• Ensembl ID: ENSMUSG00000004980
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:MGI Symbol;Acc:MGI:104819]

Sequence

>retro_mmus_573
AAGAGAGAAAAGGAAAACTTCAGCAAGCTCTTTCTTGGTGGCTTAAGCTTTGAAACCACAGAAAAAAGTTTGAGAAACTA
CTATGAACAGTGGGGAAAGCTCACAGACTGTGTAGTTACGCGCGATCCTGCAAGCAAAAGATCAAGACGATTTGGCTTTG
TAACTTTCTCATCCATGGCCGAGGTTGACGCTGCCATGGCTGCAAGGTCTCATTCCATTGATGGCAGGGAAGTTGAGCCA
AAACGTGCTGTAGCACCAGAGGAGTCTGGAAAACCAGGAGCCCATGTGACTGTGAAGAAGCTGTTTGTTGGTGGAATGAA
AGAAGATACTGAGGAACACCACCTTAGAGATTCCTTTGAAGAGTATGGAAAAATTGATACTATTGAAATAATTACCGATA
GGCAGCCTGGGAAGAAAAGAGGCTTTGGCTTTGTTACTTTTGATGACCATGATCCTGTGGATAAAATTGTCATGCCAAAT
ATCACACCATAAATCACACAATGAAGAAGTTAGAAAGGCACTGTCTAGACAAGAAATGCAGGAAGTCCAAAGTTCTAGGA
GTGGAAGAGGAAGAAACTTTGGTTTGGGGGATTCTTGTGGTGGCGGTGGCAATTTT

Alignment

ORF - retro_mmus_573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.42 %
• Parental protein coverage: 60.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARP
          .REKE.F.KLF.GGLSFETTE.SLRNYYEQWGKLTDCVV.RDPASKRSR.FGFVTFSSMAEVDAAMAAR.
Retrocopy KREKENFSKLFLGGLSFETTEKSLRNYYEQWGKLTDCVVTRDPASKRSRRFGFVTFSSMAEVDAAMAARS

Parental  HSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKR
          HSIDGR.VEPKRAVA.EESGKPGAHVTVKKLFVGG.KEDTEEHHLRD.FEEYGKIDTIEIITDRQ.GKKR
Retrocopy HSIDGREVEPKRAVAPEESGKPGAHVTVKKLFVGGMKEDTEEHHLRDSFEEYGKIDTIEIITDRQPGKKR

Parental  GFGFVTFDDHDPVDKIVL-QKYHTIN-GHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGDSRGGGGNF
          GFGFVTFDDHDPVDKIV...KYHTIN..HN.EVRKALSRQEMQEVQSSRSGRG.NFG.GDS.GGGGNF
Retrocopy GFGFVTFDDHDPVDKIVM<AKYHTIN<SHNEEVRKALSRQEMQEVQSSRSGRGRNFGLGDSCGGGGNF

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	0.68 RPM	381.33 RPM
SRP007412_cerebellum	0.61 RPM	558.40 RPM
SRP007412_heart	0.93 RPM	524.70 RPM
SRP007412_kidney	1.37 RPM	646.19 RPM
SRP007412_liver	0.68 RPM	378.55 RPM
SRP007412_testis	0.41 RPM	421.48 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_573 was not detected

EST

No EST(s) were mapped for retro_mmus_573 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_5084	255 libraries	448 libraries	358 libraries	6 libraries	5 libraries

The graphical summary, for retro_mmus_573 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_573 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_573 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005726	4 retrocopies	retro_btau_1330, retro_btau_1535, retro_btau_193, retro_btau_228,
Choloepus hoffmanni	ENSCHOG00000013832	15 retrocopies	retro_chof_1060, retro_chof_1191, retro_chof_1413, retro_chof_1460, retro_chof_1507, retro_chof_2062, retro_chof_2135, retro_chof_2235, retro_chof_2263, retro_chof_2404, retro_chof_2425, retro_chof_2473, retro_chof_2574, retro_chof_499, retro_chof_853,
Ciona intestinalis	ENSCING00000004062	1 retrocopy	retro_cint_7,
Ciona savignyi	ENSCSAVG00000000472	1 retrocopy	retro_csav_26,
Dasypus novemcinctus	ENSDNOG00000012928	1 retrocopy	retro_dnov_1978,
Dipodomys ordii	ENSDORG00000005482	1 retrocopy	retro_dord_489,
Echinops telfairi	ENSETEG00000018577	1 retrocopy	retro_etel_1368,
Felis catus	ENSFCAG00000027765	1 retrocopy	retro_fcat_692,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Myotis lucifugus	ENSMLUG00000007578	1 retrocopy	retro_mluc_34,
Mus musculus	ENSMUSG00000004980	1 retrocopy	retro_mmus_573 ,
Mus musculus	ENSMUSG00000046434	3 retrocopies	retro_mmus_1861, retro_mmus_410, retro_mmus_543,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000026859	2 retrocopies	retro_ocun_1205, retro_ocun_642,
Ochotona princeps	ENSOPRG00000011698	2 retrocopies	retro_opri_165, retro_opri_893,
Ictidomys tridecemlineatus	ENSSTOG00000006202	3 retrocopies	retro_itri_1723, retro_itri_448, retro_itri_717,
Tursiops truncatus	ENSTTRG00000000709	3 retrocopies	retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,