RetrogeneDB ID: retro_mmus_1409

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:77443751..77444420(-)
• Located in intron of: ENSMUSG00000068252

Retrocopy information

• Ensembl ID: ENSMUSG00000082233
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hnrnpa3
• Ensembl ID: ENSMUSG00000059005
• Aliases: Hnrnpa3, 2410013L13Rik, 2610209F03Rik, 2610510D13Rik, Hnrpa3
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:MGI Symbol;Acc:MGI:1917171]

Sequence

>retro_mmus_1409
ATGGAGGTAAAACCGCCACCCAGTCGCCCCCAGCCTGACTCCGGCCATTGCCACCACCGCTGGGGGGAGGAGGGCCATGA
TCCACAGGAACCAGAGCAGCTGAGGAAGCTGTTTATTGGTGGTCTGGGCTTTGAAACCACATGATGAGAGCTTACGAGAA
CATTTTGAGAAATGGGGCACACTTACAGACTGTGTGGTCATGAGAGATCCCCAAACAAAACATTCCAGAGGCTTGGGTTT
TGTGACCTACTCTCTGTGTTGAAGAAGTGGATGCTGCAATGTGTGCTCGGCCACACAAGGATGATGGATGTGTGGTGGAA
CCAAAGAGAGCTGTTTCTAGAGGATTCTGTAAAGTCTGGTGCCCATTTAATGGTGAAGAAATTTTTTGTTGGTGGTATTA
AAGAGGATACGGAAGAATATAACCTGAGAGACGGCTTTGAAAAGTATGGCAAGATTGAAACCATAGAGGTTATGGAAGAC
AGGCAGAGTGGGAAAAAGAGAGGGTTTGCTTTTGTAACTTTTGATGATCATGACACAGTTGATAAAATTGTTGTTCAGAA
ATACCACACGATTAATAGGCATAATTGTGAAGTGAAAAAGGCCCTTTCTAAACCAGAGATGCAGTCTGCTGGATCCCAGA
GAGGTCGTGGAGGTGGATATGGCAGCTTT

Alignment

ORF - retro_mmus_1409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 58.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEVKPPPGRPQPDSGRRRRRRGEEGHDPKEPEQLRKLFIGGLSFETT-DDSLREHFEKWGTLTDCVVMRD
          MEVKPPP.RPQPDSG....R.GEEGHDP.EPEQLRKLFIGGL.FETT.D.SLREHFEKWGTLTDCVVMRD
Retrocopy MEVKPPPSRPQPDSGHCHHRWGEEGHDPQEPEQLRKLFIGGLGFETT>DESLREHFEKWGTLTDCVVMRD

Parental  PQTKRSRGF-GFVTYSCVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTE
          PQTK.SRG..GF.....V.......C...H.....V....R....EDSVK.GAHL.VKK.FVGGIKEDTE
Retrocopy PQTKHSRGL<GFCDLLSVLKKWMLQCVLGHTRMMDVWWNQRELFLEDSVKSGAHLMVKKFFVGGIKEDTE

Parental  EYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQ
          EYNLRD.FEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTIN.HNCEVKKALSK.EMQ
Retrocopy EYNLRDGFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINRHNCEVKKALSKPEMQ

Parental  SAGSQRGRGGGSGNF
          SAGSQRGRGGG.G.F
Retrocopy SAGSQRGRGGGYGSF

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	111.18 RPM
SRP007412_cerebellum	0.00 RPM	170.43 RPM
SRP007412_heart	0.00 RPM	112.60 RPM
SRP007412_kidney	0.12 RPM	187.13 RPM
SRP007412_liver	0.00 RPM	100.71 RPM
SRP007412_testis	0.00 RPM	196.59 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1409 was not detected

EST

No EST(s) were mapped for retro_mmus_1409 retrocopy.

TSS

No TSS is located nearby retro_mmus_1409 retrocopy 5' end.

Lab

retro_mmus_1409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1409 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 92 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Canis familiaris	ENSCAFG00000013497	12 retrocopies	retro_cfam_1214, retro_cfam_1326, retro_cfam_1388, retro_cfam_1548, retro_cfam_1690, retro_cfam_1816, retro_cfam_265, retro_cfam_272, retro_cfam_400, retro_cfam_625, retro_cfam_65, retro_cfam_836,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
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	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pteropus vampyrus	ENSPVAG00000010380	2 retrocopies	retro_pvam_1077, retro_pvam_326,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Sus scrofa	ENSSSCG00000015988	6 retrocopies	retro_sscr_1110, retro_sscr_1152, retro_sscr_391, retro_sscr_621, retro_sscr_764, retro_sscr_927,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,