RetrogeneDB ID:

retro_mmus_210

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:3:54481465..54482539(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000069014
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Hnrnpa3
Ensembl ID:ENSMUSG00000059005
Aliases:Hnrnpa3, 2410013L13Rik, 2610209F03Rik, 2610510D13Rik, Hnrpa3
Description:heterogeneous nuclear ribonucleoprotein A3 [Source:MGI Symbol;Acc:MGI:1917171]


Retrocopy-Parental alignment summary:






>retro_mmus_210
ATGGAGGGCCATGATCCAAAGGAACCAGAGCAGCTGAGGAAGCTATTTATTGGTGGTCTGAGCTTTGAAACCACAGATGA
TAGCTTAAGAGAACATTTTGAGAAATGGGGCACACTTACAGACTGTGTGGTAATGAGAGATCCCCAAACAAAACGTTCCA
GAGGCTTTGGTTTTGTGACCTACTCTTGTGTTGAAGAGGTGGATGCTGCAATGTGTGCTCGGCCACACAAGGTTGATGGG
CGTGTGGTGGAACCGAAGAGAGCTGTTTCTAGAGAGGATTCTGTAAAGCCTGGTGCCCATTTAACGGTGAAGAAAATTTT
TGTTGGTGGTATTAAAGAGGATACGGAAGAATATAACCTGAGAGACTACTTTGAAAAGTATGGCAAGATTGAAACCATAG
AGGTTATGGAAGACAGGCAGAGTGGGAAAAAGAGAGGATTTGCTTTTGTAACTTTTGATGATCATGACACAGTTGATAAA
ATTGTTGTTCAGAAATACCACACTATTAATGGGCATAATTGTGAAGTGAAAAAGGCCCTTTCTAAACAAGAGATGCAGTC
TGCTGGATCACAGAGAGGTCGTGGAGGTGGATCTGGCAACTTTATGGGTCGTGGAGGAAACTTTGGAGGTGGTGGAGGAA
ACTTTGGTCGTGGAGGAAACTTTGGTGGAAGAGGTGGCTATGGTGGTGGAGGTGGTGGCAGCAGAGGTAGTTATGGAGGT
GGTGATGGTGGATATAATGGATTTGGAGGTGATGGTGGCAACTATGGTGGTGGTCCTGGTTACAGCAGTAGAGGAGGTTA
TGGAGGTGGTGGACCAGGATATGGAAACCAGGGTGGTGGATATGGTGGTGGAGGAGGAGGCTATGATGGTTACAATGAAG
GAGGAAATTTTGGTGGAGGTAACTATGGTGGTGGTGGAAACTATAATGACTTTGGAAATTATAGTGGACAGCAACAATCA
AATTATGGACCCATGAAGGGGGGCAGTTTTGGTGGAAGAAGCTCAGGCAGTCCCTATGGTGGTGGCTATGGATCTGGAGG
TGGAAGTGGTGGATATGGTAGCAGAAGGTTTTAA

ORF - retro_mmus_210 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100. %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
MEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
RetrocopyMEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
ParentalMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQ
MCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQ
RetrocopyMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQ
ParentalSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFGG
SGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFGG
RetrocopySGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFGG
ParentalGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQGGG
GGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQGGG
RetrocopyGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQGGG
ParentalYGGGGGGYDGYNEGGNFGGGNYGGGGNYNDFGNYSGQQQSNYGPMKGGSFGGRSSGSPYGGGYGSGGGSG
YGGGGGGYDGYNEGGNFGGGNYGGGGNYNDFGNYSGQQQSNYGPMKGGSFGGRSSGSPYGGGYGSGGGSG
RetrocopyYGGGGGGYDGYNEGGNFGGGNYGGGGNYNDFGNYSGQQQSNYGPMKGGSFGGRSSGSPYGGGYGSGGGSG
ParentalGYGSRRF
GYGSRRF
RetrocopyGYGSRRF

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 .00 RPM 187 .13 RPM
SRP007412_liver 0 .00 RPM 100 .71 RPM
SRP007412_testis 0 .23 RPM 196 .59 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_210 was not detected

EST - click to see more details

15 EST(s) were mapped to retro_mmus_210 retrocopy
EST ID Start End Identity Match Mis-match Score
AA212389 54481453 54481780 100 327 0 327
AV483745 54481445 54481794 100 346 0 343
AV581043 54481452 54481881 100 429 0 429
AV582174 54481429 54481944 100 514 0 513
AW209984 54481427 54481746 100 319 0 319
BE308256 54481447 54481956 100 508 0 507
BU581931 54481441 54481963 100 522 0 522
BY141011 54481425 54481759 100 334 0 334
CA564862 54481427 54481982 100 555 0 555
CA882508 54481429 54481946 100 517 0 517
CD539593 54481466 54482047 100 581 0 581
CF906682 54481445 54482026 100 581 0 581
CF907855 54481535 54482092 100 557 0 557
CJ055419 54481417 54481830 100 413 0 413
CO045185 54481433 54481827 100 394 0 394

TSS - click to see more details

No TSS is located nearby retro_mmus_210 retrocopy 5' end.

Lab - click to see more details

retro_mmus_210 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_210 has 0 orthologous retrocopies within eutheria group .

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

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000215808 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 ENSCAFG0000001349712 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 ENSDNOG000000190223 retrocopies
retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis ENSFALG000000032151 retrocopy
retro_falb_15,
Felis catus ENSFCAG000000121465 retrocopies
retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens ENSG0000017014411 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 ENSGALG000000092501 retrocopy
retro_ggal_10,
Gorilla gorilla ENSGGOG000000061306 retrocopies
retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii ENSMEUG000000136226 retrocopies
retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta ENSMMUG000000018584 retrocopies
retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus ENSMUSG000000049801 retrocopy
retro_mmus_573,
Mus musculus ENSMUSG000000464343 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 ENSOCUG000000027432 retrocopies
retro_ocun_994, retro_ocun_995,
Otolemur garnettii ENSOGAG000000281327 retrocopies
retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Pelodiscus sinensis ENSPSIG000000030111 retrocopy
retro_psin_16,
Pteropus vampyrus ENSPVAG000000103802 retrocopies
retro_pvam_1077, retro_pvam_326,
Sarcophilus harrisii ENSSHAG000000182551 retrocopy
retro_shar_518,
Sus scrofa ENSSSCG000000159886 retrocopies
retro_sscr_1110, retro_sscr_1152, retro_sscr_391, retro_sscr_621, retro_sscr_764, retro_sscr_927,
Ictidomys tridecemlineatus ENSSTOG000000251254 retrocopies
retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis ENSXETG000000018061 retrocopy
retro_xtro_11,
Xiphophorus maculatus ENSXMAG000000004391 retrocopy
retro_xmac_2,


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