RetrogeneDB ID:

retro_mmus_283

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:13:111255132..111256263(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000055194
Aliases:Actbl2, 4732495G21Rik
Status:KNOWN_PROTEIN_CODING
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_283
ATGGTTGACGATGAGCTGACTGCTTTGGTAGTAGATAATGGGTCAGGGATGTGCAAGGCAGGTTTTGGGGGTGACGATGC
CCCCCGTGCTGTGTTCCCCTCCATGGTTGGTCGTCCACGACACCAGGGGGTCATGGTAGGCATGGGCCAGAAGGACTGTT
ATGTGGGAGATGAGGCCCAGAGCAAGCGAGGCATCTTGACCTTGAAGTATCCCATTGAACACGGAGTCGTCACCAACTGG
GATGATATGGAGAAGATCTGGTACCACACTTTCTACAATGAGCTCCGGGTAGCACCGGATGAACATCCTATTCTTCTCAC
CGAGGCACCCCTTAACCCCAAAATCAACCGGGAAAAGATGACTCAGATAATGTTCGAGGCTTTCAACACACCTGCCATGT
ATGTAGCAATCCAAGCCGTGCTATCCCTCTATGCTTCCGGAAGGACTACAGGTATCGTGATGGATTCTGGGGATGGGGTC
ACTCACACTGTGCCTATCTATGAAGGTTACGCTCTGCCTCATGCCATTCTACGACTAGATCTGGCAGGTAGGGACCTGAC
TGATTACCTCATGAAGATTCTGACAGAACGAGGCTATAACTTCACCACCACAGCAGAGAGGGAGATCGTGCGGGATGTCA
AAGAAAAGTTGTGCTACGTGGCCCTGGACTTTGAGCAGGAGATGGTCACTGCAGCCGCTTCATCCTCACTAGAGAGAAGC
TATGAGCTCCCTGATGGGCAGGTGATCACCATTGGAAATGAACGCTTCCGGTGCCCAGAAGCCATTTTCCAGCCTTCCTT
TCTAGGCATTGAATCCAGAGGCATCCATGAGACAACCTTCAACTCGATCATGAAGTGTGATGTAGATATTCGTAAGGATT
TATTTGCCAACACTGTGCTGTCTGGAGGCAGTACCATGTACCCAGGCATTGCCGACAGGATGCAGAAGGAAATTGTAACC
TTGGCACCAAGTACCATGAAAATTAAGATCATAGCTCCCCCAGAACGCAAGTATTCGGTTTGGATTGGGGGCTCCATCCT
CGCCAGCCTGTCCACATTCCAGCAGATGTGGATCAGTAAGCAGGAATATGACGAAGCTGGACCTCCCATTGTTCATAGAA
AATGCTTCTAG

ORF - retro_mmus_283 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.8 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
.DD...ALVVDNGSGMCKAGF.GDDAPRAVFPS.VGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTLKYP
RetrocopyVDDELTALVVDNGSGMCKAGFGGDDAPRAVFPSMVGRPRHQGVMVGMGQKDCYVGDEAQSKRGILTLKYP
ParentalIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
IEHG.VTNWDDMEKIW.HTFYNELRVAP.EHP.LLTEAPLNPK.NREKMTQIMFE.FNTPAMYVAIQAVL
RetrocopyIEHGVVTNWDDMEKIWYHTFYNELRVAPDEHPILLTEAPLNPKINREKMTQIMFEAFNTPAMYVAIQAVL
ParentalSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGY.FTTTAEREIVR
RetrocopySLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYNFTTTAEREIVR
ParentalDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
D.KEKLCYVALDFEQEM.TAA.SSSLE.SYELPDGQVITIGNERFRCPEA.FQPSFLG.ES.GIHETTFN
RetrocopyDVKEKLCYVALDFEQEMVTAAASSSLERSYELPDGQVITIGNERFRCPEAIFQPSFLGIESRGIHETTFN
ParentalSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
SIMKCDVDIRKDL.ANTVLSGG.TMYPGIADRMQKEI..LAPSTMKIKIIAPPERKYSVWIGGSILASLS
RetrocopySIMKCDVDIRKDLFANTVLSGGSTMYPGIADRMQKEIVTLAPSTMKIKIIAPPERKYSVWIGGSILASLS
ParentalTFQQMWISKQEYDESGPSIVHRKCF
TFQQMWISKQEYDE.GP.IVHRKCF
RetrocopyTFQQMWISKQEYDEAGPPIVHRKCF

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 .02 RPM 922 .02 RPM
SRP007412_cerebellum 0 .65 RPM 706 .77 RPM
SRP007412_heart 0 .00 RPM 464 .18 RPM
SRP007412_kidney 0 .00 RPM 679 .61 RPM
SRP007412_liver 0 .00 RPM 437 .32 RPM
SRP007412_testis 0 .37 RPM 567 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_283 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_283 retrocopy.

TSS - click to see more details



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_265901056 libraries 10 libraries 2 libraries 2 libraries 2 libraries

The graphical summary, for retro_mmus_283 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)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_283 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_283 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_38
Pan troglodytes retro_ptro_53
Gorilla gorilla retro_ggor_1297
Pongo abelii retro_pabe_86
Callithrix jacchus retro_cjac_243
Rattus norvegicus retro_rnor_351
Oryctolagus cuniculus retro_ocun_38
Bos taurus retro_btau_903
Canis familiaris retro_cfam_934
Equus caballus retro_ecab_98
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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