RetrogeneDB ID:

retro_mmus_1613

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:17:8565892..8566945(-)
Located in intron of:ENSMUSG00000023868
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Actb
Ensembl ID:ENSMUSG00000029580
Aliases:Actb, Actx, E430023M04Rik, beta-actin
Description:actin, beta [Source:MGI Symbol;Acc:MGI:87904]


Retrocopy-Parental alignment summary:






>retro_mmus_1613
ATAAATGATGATATCACTGTGCTAGTCAACGTTGACAATGGCTCTGGCTTGTGCAAAGCTGCCTTTGCGAGCGACGATGC
TTCCCCAGGCCATCTTCCCCTCCATCGTGGGCCTCCCTAGGCACCAGGGTATGATGGTGGGTATGGGTCAGAGGGACTCT
TATGTGGGCGACGAGGCCCAAAGCAAGAGAGGCTTCCTGACCCTGAAGTACCCCATTGAACATGGCATTGTCACCAACTG
GGACAATATAAAGAAGGTCTGGCACCATACCTTTTACAATGAGCTGCGTGTGGCCCCTGAGGAGTACCCTGTACTGCTCA
CTGAAGGCCCCCTGAACCCTAAGGCCAACCGTGAAAAGATGACCCAGATCATGTTTGAGACCTTCAACATCCCAGCCATG
TACAACGCCATCCAGGCTGTGTTGTCCCTATATGCATCTGGTTGTACCACTGGTATTTTGATGGACTTCAGAGATGGGTT
ACCCACATTATGCCCATCTACGAGGGCTATGCCATGCTGTGTCTGGACCTGGCTGGCCGGGACCTGACAGTGTACCTCAT
GAAGATCCTGACCCAGCGTGGCTACAGCTTCACCAACATGGCTGAGAGGGAAATCATGCGTGACAAAGAGAAGCTGTGCT
ATGTTGCCCTAGACTTTGAGCAGGAGATGGCCACTGCCGCATTCTCTTCTTCCCTGGAGAAGAGCTATAAGCTGCCTGAC
AGACAGGTCATCACTATTGGCAATAAGCGGTTCCAATGCCCTGGGGCTCTTTTCCAGCCTTCCTTCTTGAGTATGGAATC
CTGTGGCATCCATGAAACTACATTCAATTCCATCATGAAGTATGACATTGACATTTGTAAAGACTTCTATGCCAACACAG
TGCTATCTGGTAGCACCACTATGCACCCAAACATTGCTGACAGGATGCAGAAGGAGATCACTGCTCTAGATCCTAGCACC
AAGAAGACCAAGATCATTGCTCCTCCTAAGCTCAGGTACTCTGTGTAGATCAGTGGCTCCATCCTGGCCTCCACCTTCCA
GCAGACGTGGATC

ORF - retro_mmus_1613 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.39 %
Parental protein coverage: 95.2 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMDDDIAALV-VDNGSGMCKAGFAGDDA-PRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK
..DDI..LV.VDNGSG.CKA.FA.DDA.P.A.FPSIVG.PRHQG.MVGMGQ.DSYVGDEAQSKRG.LTLK
RetrocopyINDDITVLVNVDNGSGLCKAAFASDDA>PQAIFPSIVGLPRHQGMMVGMGQRDSYVGDEAQSKRGFLTLK
ParentalYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQA
YPIEHGIVTNWD...K.WHHTFYNELRVAPEE.PVLLTE.PLNPKANREKMTQIMFETFN.PAMY.AIQA
RetrocopyYPIEHGIVTNWDNIKKVWHHTFYNELRVAPEEYPVLLTEGPLNPKANREKMTQIMFETFNIPAMYNAIQA
ParentalVLSLYASGRTTGIVMDSGDG-VTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAERE
VLSLYASG.TTGI.MD..DG.VTH..PIYEGYA.....L.LDLAGRDLT.YLMKILT.RGYSFT..AERE
RetrocopyVLSLYASGCTTGILMDFRDG<VTHIMPIYEGYAM----LCLDLAGRDLTVYLMKILTQRGYSFTNMAERE
ParentalIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHET
I.RD.KEKLCYVALDFEQEMATAA.SSSLEKSY.LPD.QVITIGN.RF.CP.ALFQPSFL.MESCGIHET
RetrocopyIMRD-KEKLCYVALDFEQEMATAAFSSSLEKSYKLPDRQVITIGNKRFQCPGALFQPSFLSMESCGIHET
ParentalTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILA
TFNSIMK.D.DI.KD.YANTVLSG.TTM.P.IADRMQKEITAL.PST.K.KIIAPP...YSV.I.GSILA
RetrocopyTFNSIMKYDIDICKDFYANTVLSGSTTMHPNIADRMQKEITALDPSTKKTKIIAPPKLRYSV*ISGSILA
ParentalSLSTFQQMWI
..STFQQ.WI
Retrocopy--STFQQTWI

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 .21 RPM 922 .02 RPM
SRP007412_cerebellum 0 .48 RPM 706 .77 RPM
SRP007412_heart 0 .16 RPM 464 .18 RPM
SRP007412_kidney 0 .25 RPM 679 .61 RPM
SRP007412_liver 0 .03 RPM 437 .32 RPM
SRP007412_testis 0 .14 RPM 567 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_1613 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1613 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1613 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1613 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1613 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 96 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066011 retrocopy
retro_amel_11,
Cavia porcellus ENSCPOG000000134671 retrocopy
retro_cpor_60,
Homo sapiens ENSG000000756246 retrocopies
retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus ENSGALG000000096211 retrocopy
retro_ggal_4,
Gorilla gorilla ENSGGOG0000000113318 retrocopies
retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Meleagris gallopavo ENSMGAG000000039602 retrocopies
retro_mgal_5, retro_mgal_6,
Macaca mulatta ENSMMUG000000111531 retrocopy
retro_mmul_135,
Mustela putorius furoENSMPUG000000166122 retrocopies
retro_mputfur_440, retro_mputfur_461,
Mus musculus ENSMUSG000000252281 retrocopy
retro_mmus_2686,
Mus musculus ENSMUSG00000029580 7 retrocopies
retro_mmus_1613 , retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Mus musculus ENSMUSG000000628257 retrocopies
retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Ornithorhynchus anatinus ENSOANG000000077162 retrocopies
retro_oana_4, retro_oana_8,
Otolemur garnettii ENSOGAG000000083481 retrocopy
retro_ogar_2637,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000001733623 retrocopies
retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus ENSRNOG0000003425410 retrocopies
retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii ENSSHAG000000126944 retrocopies
retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa ENSSSCG000000075851 retrocopy
retro_sscr_548,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus ENSSTOG000000147973 retrocopies
retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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