RetrogeneDB ID:

retro_mmus_227

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:6:128644912..128646391(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000037827
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Tom1
Ensembl ID:ENSMUSG00000042870
Aliases:None
Description:target of myb1 homolog (chicken) [Source:MGI Symbol;Acc:MGI:1338026]


Retrocopy-Parental alignment summary:






>retro_mmus_227
ATGGACTTTCTCCTGGGAAATCCGTTCAGCTCTCCGGTGGGACAACGGATCGAGAAAGCTACAGATGGCTCCCTGCAGAG
CGAGGACTGGGCCCTCAACATGGAAATCTGTGACATCATCAACGAGACGGAGGAAGGCCCCAAAGATGCCTTCCGAGCAG
TGAAGAAGCGAATTATGGGGAATAAGAATTTCCATGAGGTCATGCTGGCCCTTACGGTCTTGGAAACATGTGTTAAGAAC
TGTGGGCACCGCTTCCATGTACTGGTGGCCAACCAGGACTTTGTAGAGAATGTGCTGGTGAGGACCATCCTGCCGAAGAA
CAATCCACCCACCATTGTGCATGACAAGGTGTTGAACCTCATCCAGTCCTGGGCTGACGCGTTCCGCAGCTCACCTGATT
TGACAGGTGTTGTTGCTGTCTACGAGGACCTGCGAAGGAAGGGCCTAGAATTTCCCATGACTGACCTGGACATGCTGTCG
CCCATCCACACACCCCAGAGAACTGTATTCAACTCAGAGACACCATCCAGACAGAACTCTGTGAGTTCCAACACCAGTCA
GCGTGGAGACCTGAGCCAGCATGCCACCCCTCTGCCCACTCCAGCTGTTCTCCCGGGTGACTCACCCATCACACCGACTC
CTGAGCAGATTGGGAAGCTGCGCAGTGAGCTGGAGATGGTGAGCGGAAACGTGCGAGTGATGTCAGAGATGCTGACAGAG
CTGGTGCCCACCCAGGTAGAGCCTGCAGACCTGGAGCTACTACAGGAACTGAACCGCACCTGCCGTGCCATGCAGCAGCG
GATCCTGGAGCTTATCCCACGCATCTCCAATGAGCAGCTGACGGAGGAGCTGCTCATGATCAACGACAACCTCAACAACG
TGTTTCTGCGCCATGAACGGTTTGAACGCTTCCGAACAGGCCAGACTGCTAAGGCCTCCAGTGAAGCTGAGCTAGCTACT
GACCTGATTGACATGGGTCCTGACCCCGCAGCCACAAACAACCTCTCATCTCAACTGGCAGGAATGAACCTTGGCTCCAG
AAGTGTGAGAGCTGGCCTGCAGTCTCTGGAGACCTCAGGTCACCTGGAAGATGACTTTGACATGTTTGCTCTGACTCGGG
GCAGCTCACTGGCTGACCAACGGAAAGGGGTCAAATATGAAGCTCCCCAAACCACAGATGGCCTGGCTGGGGCCCTAGAT
GCCCGGCAGCAGAGCACCGGAGCGATCCCAGCCACTCAGGCCCGCATCATGGAGGACATTGAGCAGTGGCTGTCCACAGA
TGTGGGGAACAGTGCTGAGGAGCCCTCTGGTGTCACCAGTGAAGAATTTGACAAATTTCTGGAAGAACGAGCCAAAGCTG
CTGATCGACTTCCCAACCTGGCCAGCCCTTCAGCCGAGGGACCCCCCAGACCATCTCCTGGAACAGCCCCTCGGAGGAAG
ACCCAGGAGAAGGACGATGACATGCTGTTTGCCTTATGA

ORF - retro_mmus_227 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:

ParentalMDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDAFRAVKKRIMGNKNFHEVMLA
MDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDAFRAVKKRIMGNKNFHEVMLA
RetrocopyMDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDAFRAVKKRIMGNKNFHEVMLA
ParentalLTVLETCVKNCGHRFHVLVANQDFVENVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVAV
LTVLETCVKNCGHRFHVLVANQDFVENVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVAV
RetrocopyLTVLETCVKNCGHRFHVLVANQDFVENVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVAV
ParentalYEDLRRKGLEFPMTDLDMLSPIHTPQRTVFNSETPSRQNSVSSNTSQRGDLSQHATPLPTPAVLPGDSPI
YEDLRRKGLEFPMTDLDMLSPIHTPQRTVFNSETPSRQNSVSSNTSQRGDLSQHATPLPTPAVLPGDSPI
RetrocopyYEDLRRKGLEFPMTDLDMLSPIHTPQRTVFNSETPSRQNSVSSNTSQRGDLSQHATPLPTPAVLPGDSPI
ParentalTPTPEQIGKLRSELEMVSGNVRVMSEMLTELVPTQVEPADLELLQELNRTCRAMQQRILELIPRISNEQL
TPTPEQIGKLRSELEMVSGNVRVMSEMLTELVPTQVEPADLELLQELNRTCRAMQQRILELIPRISNEQL
RetrocopyTPTPEQIGKLRSELEMVSGNVRVMSEMLTELVPTQVEPADLELLQELNRTCRAMQQRILELIPRISNEQL
ParentalTEELLMINDNLNNVFLRHERFERFRTGQTAKASSEAELATDLIDMGPDPAATNNLSSQLAGMNLGSRSVR
TEELLMINDNLNNVFLRHERFERFRTGQTAKASSEAELATDLIDMGPDPAATNNLSSQLAGMNLGSRSVR
RetrocopyTEELLMINDNLNNVFLRHERFERFRTGQTAKASSEAELATDLIDMGPDPAATNNLSSQLAGMNLGSRSVR
ParentalAGLQSLETSGHLEDDFDMFALTRGSSLADQRKGVKYEAPQTTDGLAGALDARQQSTGAIPATQARIMEDI
AGLQSLETSGHLEDDFDMFALTRGSSLADQRKGVKYEAPQTTDGLAGALDARQQSTGAIPATQARIMEDI
RetrocopyAGLQSLETSGHLEDDFDMFALTRGSSLADQRKGVKYEAPQTTDGLAGALDARQQSTGAIPATQARIMEDI
ParentalEQWLSTDVGNSAEEPSGVTSEEFDKFLEERAKAADRLPNLASPSAEGPPRPSPGTAPRRKTQEKDDDMLF
EQWLSTDVGNSAEEPSGVTSEEFDKFLEERAKAADRLPNLASPSAEGPPRPSPGTAPRRKTQEKDDDMLF
RetrocopyEQWLSTDVGNSAEEPSGVTSEEFDKFLEERAKAADRLPNLASPSAEGPPRPSPGTAPRRKTQEKDDDMLF
ParentalAL
AL
RetrocopyAL

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 .07 RPM 4 .11 RPM
SRP007412_cerebellum 0 .13 RPM 4 .08 RPM
SRP007412_heart 0 .44 RPM 10 .30 RPM
SRP007412_kidney 0 .19 RPM 6 .60 RPM
SRP007412_liver 0 .16 RPM 3 .66 RPM
SRP007412_testis 0 .18 RPM 10 .20 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_227 was not detected

EST - click to see more details

73 EST(s) were mapped to retro_mmus_227 retrocopy
EST ID Start End Identity Match Mis-match Score
AA388933 128644887 128645433 99.9 544 0 541
AA463074 128644857 128645303 99.6 444 2 442
AA592451 128644867 128645486 100 467 0 464
AA656929 128644889 128645445 99.8 389 0 385
AI664521 128644884 128645476 99.5 587 2 583
AW457392 128644857 128645227 100 370 0 370
BB656379 128644841 128645403 99 554 5 546
BB855166 128644873 128645349 99.8 475 1 474
BB855766 128644899 128645392 100 493 0 493
BE290228 128644917 128645532 98.9 607 7 599
BE849518 128644874 128645571 99.5 381 2 378
BE948382 128644857 128645227 100 370 0 370
BF469415 128645021 128645440 100 419 0 419
BF582751 128644871 128645538 99.4 656 3 644
BG082477 128644897 128645461 100 564 0 564
BG796721 128645119 128645564 98.7 426 6 415
BI452669 128644850 128645559 99.3 703 5 697
BI693400 128645041 128645742 100 700 0 699
BI872084 128644918 128645729 99.7 802 2 792
BM935331 128644858 128645223 100 365 0 365
BQ258180 128644890 128645555 100 665 0 665
BQ266756 128644893 128645408 100 515 0 515
BX526426 128644883 128645406 100 523 0 523
BY000536 128644884 128645296 99 393 4 388
BY020933 128644863 128645237 99.2 371 3 368
BY077578 128644869 128645241 100 372 0 372
BY080384 128644841 128645210 100 368 0 368
BY082888 128644860 128645236 99.3 373 3 370
BY084957 128644842 128645201 100 359 0 359
BY087901 128644860 128645239 100 379 0 379
BY114739 128644876 128645208 100 332 0 332
BY114752 128644876 128645193 100 317 0 317
BY122432 128644860 128645163 100 303 0 303
BY133290 128644876 128645240 99.8 363 1 362
BY172224 128644860 128645217 98.1 350 7 343
BY229804 128644841 128645215 99.8 373 1 372
BY240445 128644860 128645392 99.4 449 3 445
BY256016 128644863 128645622 100 445 0 444
BY256900 128644884 128645433 96.6 450 14 431
BY256915 128644884 128645438 99.2 466 4 461
BY257524 128644884 128645429 99.2 460 4 455
BY261427 128644876 128645327 99.6 448 2 446
BY267376 128644846 128645234 100 388 0 388
BY270637 128644846 128645276 100 430 0 430
BY272523 128644876 128645309 100 433 0 433
BY281327 128644841 128645271 99.8 429 1 428
BY316054 128644841 128645217 99.5 374 2 372
BY320119 128644841 128645213 100 372 0 372
BY346472 128644876 128645188 99.7 310 1 309
BY779510 128644860 128645295 97.2 349 7 338
BY782058 128644860 128645270 99.4 329 2 326
BY789663 128644860 128645277 99.8 337 1 335
CA531936 128644991 128645502 99.9 510 1 509
CA533933 128644843 128645660 100 503 0 502
CA542181 128644895 128645389 99.6 492 2 490
CA548913 128644897 128645318 99.8 420 1 419
CA549695 128644897 128645412 100 515 0 515
CA554147 128644897 128645412 100 515 0 515
CA562541 128644885 128645321 100 436 0 436
CF153923 128644897 128645433 100 536 0 536
CF900161 128644854 128645544 100 690 0 690
CJ067650 128644863 128645335 99.8 471 1 470
CJ067786 128644863 128645320 99.6 455 2 453
CJ134695 128644876 128645503 100 626 0 625
CJ134877 128644876 128645507 100 630 0 629
CJ139478 128644860 128645348 100 488 0 488
CJ162451 128644869 128645328 100 459 0 459
CJ164904 128644876 128645301 100 407 0 406
CJ184744 128644876 128645297 100 403 0 402
CK333620 128644897 128645302 99.8 404 1 403
CN684810 128645088 128645738 99.9 649 1 648
CX230135 128645090 128645412 98.5 314 5 306
DN176210 128644901 128645226 99.7 324 1 323

TSS - click to see more details

No TSS is located nearby retro_mmus_227 retrocopy 5' end.

Lab - click to see more details

retro_mmus_227 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_227 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000042870 1 retrocopy
retro_mmus_227 ,


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