RetrogeneDB ID:

retro_mmus_24

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:10:72309320..72311159(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000053830
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Hbs1l
Ensembl ID:ENSMUSG00000019977
Aliases:Hbs1l, 2810035F15Rik, AI326327, eRFS
Description:Hbs1-like (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1891704]


Retrocopy-Parental alignment summary:






>retro_mmus_24
ATGGCCCGGCATCGGAACGTCCGGGGATATAACTACGATGAAGATTTTGAAGATGATGATCTGTATGGGCAGTCTGTGGA
GGATGACTACTGTATCTCACCATCAACAGCCGCTCAGTTCATTTACTCACGCCGTGACAACCCTGAAGAAGAATATGGCT
ATGAAGATCTGAGAGAGTCTTCTAATTCTCTTTTGAATCACCAATTAAGTGAAATTGACCAAGCTCGCCTGTATTCATGC
CTTGATCACATGAGAGAGGTACTGGGGGACGCTGTGCCTGATGACATACTGACTGAGGCAATTCTGAAACACAAATTTGA
TGTGCAGAAGGCTTTGTCCGTGGTTCTGGAACAAGATGGTGTGCAGCCTTGGAAGGAGAAGAGTGAGCGAGCAGTGTGTG
CAGGACAGCCTTCAAAAGGAGTCTTATTTTCTTCCTTTGGAGTTTCACCCCAAAATGTTCACCATTCTTATCTTCAATCA
GAAAATCATTTGGATAGCAGTAGCAAACCTTTTGATTGTTGTAGCTCAATAGCAGAATATGGATCCCATAGTTCTTCACT
TGAGCCACGTCACTATTTACTTCATAGAAAAGAGAAACATGACAGACCCCAAAGTGAAAAGGAACTAGAATCATGTAAGT
TAACAAAAGAGCTGGCTCTAGCTCACCTGATTCATGATACGCCAAGAGATTCTTGTGCACGCCAGCTGTCAGCCAGACTG
CCACCCTCAGACAGCGGGCAGAGTGAGCTTCTTAAGAGCCTAGGTGCTGATGTGGTAAGACCTCCTGCATCTGCGTGTGC
TCCTGAAGAGGATTTTACTTTCAAAGGGATACGAGACTTAGAGTCCCTAGTGAGGGAGGACGTAGTAACTAGTGGTTCTT
TGGGAATTCGGAGCAGCTCACTACCTGATTTTCAAAGTACTCCCGTGCAGAACGTCTCAGCAAGCTTAAGTAATCCACTG
CTGTTATCTAGCCCAGTGGAAAATAATTCCAGTATAAACACTGAAGTTGAACAAAGTGCCAAGAATAATATTGTAAAAAC
TAACAGTTTACCATTTTCCCAGCGTGAAAGTCCATCCCTAGCTGAGCTGTTTGAGGAACACAGAGGAAGCAGCTCTGGCC
AGTGCTTTACTTTGTCTGACCTGTGTAACCAGTCACCTGCCAGCTTGGGTTCCCTTCCCCTGTCACAACTGGCAAACCGC
TCGCAGTCTGCTAACGGAGTATCAGAGTTAACAGGATCTCTGTCATCTTTGGCATTTTGTAAAGCTGCCCCCACGAGAGA
CCTGGAGAATTTATCCCTTTCTGATTTGATTGCAAAAACGATTGGACTAGACAATTCTCAGATTAACAGAGATTCCTTTG
AGTTTAGTTTATCTGAAACTATGAGGAGCCCTGAAGTTGATTCAAATATTGATCTTAGTGTCTTGATAAAAACTCCAGAG
TTTGTCCCAAAGCCTGTAGTTGACCCATCAGTTGCTGTAACACCAGACACTAAAGTTCTGAGTTCAAAGTTAGGGAAACC
TTCCAATTCTACTAAGGATAGTATGAAACCCAAAAGAGCCTCCCTTGCTAGGAAAGCTCCTCTGTCTCTGCCGTGGACCA
AGGCCCTTGCTGCTAGGCCTTCAGCTTTCGCGTCAACGCTGTGTCTTCGTTACCCACTGAAAAGCTGCAAGAGGCGCACT
CTTGAACTCTACAAGACTTTCCTTTATAGCAGACAAGTTCAAGATGTATCGGACAAAGAAATAAGTCCTCTTGCAGCAAT
AACGCCATTTGACTTCAAATCAGCATCTCCTGATGACGTTGTAAAAGCTAATCAAAAGAAGGCGTTTACTAGAGAATAG

ORF - retro_mmus_24 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.84 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMARHRNVRGYNYDEDFEDDDLYGQSVEDDYCISPSTAAQFIYSRRDNPEEEYGYEDLRESSNSLLNHQLS
MARHRNVRGYNYDEDFEDDDLYGQSVEDDYCISPSTAAQFIYSRRDNPEEEYGYEDLRESSNSLLNHQLS
RetrocopyMARHRNVRGYNYDEDFEDDDLYGQSVEDDYCISPSTAAQFIYSRRDNPEEEYGYEDLRESSNSLLNHQLS
ParentalEIDQARLYSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQDGVQPWKEKSERAVCAGQPSKG
EIDQARLYSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQDGVQPWKEKSERAVCAGQPSKG
RetrocopyEIDQARLYSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQDGVQPWKEKSERAVCAGQPSKG
ParentalVLFSSFGVSPQNVHHSYLQSENHLDSSSKPFDCCSSIAEYGSHSSSLEPRHYLLHRKEKHDRPQSEKELE
VLFSSFGVSPQNVHHSYLQSENHLDSSSKPFDCCSSIAEYGSHSSSLEPRHYLLHRKEKHDRPQSEKELE
RetrocopyVLFSSFGVSPQNVHHSYLQSENHLDSSSKPFDCCSSIAEYGSHSSSLEPRHYLLHRKEKHDRPQSEKELE
ParentalSCKLTKELALAHLIHDTPRDSCARQLSARLPPSDSGQSELLKSLGADVVRPPASACAPEEDFTFKGIRDL
SCKLTKELALAHLIHDTPRDSCARQLSARLPPSDSGQSELLKSLGADVVRPPASACAPEEDFTFKGIRDL
RetrocopySCKLTKELALAHLIHDTPRDSCARQLSARLPPSDSGQSELLKSLGADVVRPPASACAPEEDFTFKGIRDL
ParentalESLVREDVVTSGSLGIRSSSLPDFQSTPVQNVSASLSNPLLLSSPVENNSSINTEVEQSAKNNIVKTNSL
ESLVREDVVTSGSLGIRSSSLPDFQSTPVQNVSASLSNPLLLSSPVENNSSINTEVEQSAKNNIVKTNSL
RetrocopyESLVREDVVTSGSLGIRSSSLPDFQSTPVQNVSASLSNPLLLSSPVENNSSINTEVEQSAKNNIVKTNSL
ParentalPFSQRESPSLAELFEEHRGSSSGQCFTLSDLCNQSPASLGSLPLSQLANRSQSANGVSELTGSLSSLAFC
PFSQRESPSLAELFEEHRGSSSGQCFTLSDLCNQSPASLGSLPLSQLANRSQSANGVSELTGSLSSLAFC
RetrocopyPFSQRESPSLAELFEEHRGSSSGQCFTLSDLCNQSPASLGSLPLSQLANRSQSANGVSELTGSLSSLAFC
ParentalKAAPTRDLENLSLSDLIAKTIELDNSQINRDSFEFSLSETMRSPEVDSNIDLSVLIKTPEFVPKPVVDPS
KAAPTRDLENLSLSDLIAKTI.LDNSQINRDSFEFSLSETMRSPEVDSNIDLSVLIKTPEFVPKPVVDPS
RetrocopyKAAPTRDLENLSLSDLIAKTIGLDNSQINRDSFEFSLSETMRSPEVDSNIDLSVLIKTPEFVPKPVVDPS
ParentalVAVTPDTKVLSSKLGKPSNSTKDSMKPKRASLARKAPLSLPWTKALAARPSAFASTLCLRYPLKSCKRRT
VAVTPDTKVLSSKLGKPSNSTKDSMKPKRASLARKAPLSLPWTKALAARPSAFASTLCLRYPLKSCKRRT
RetrocopyVAVTPDTKVLSSKLGKPSNSTKDSMKPKRASLARKAPLSLPWTKALAARPSAFASTLCLRYPLKSCKRRT
ParentalLELYKTFLYSRQVQDVSDKEISPLAAITPFDFKSASPDDVVKANQKKAFTRE
LELYKTFLYSRQVQDVSDKEISPLAAITPFDFKSASPDDVVKANQKKAFTRE
RetrocopyLELYKTFLYSRQVQDVSDKEISPLAAITPFDFKSASPDDVVKANQKKAFTRE

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






(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 37 .50 RPM
SRP007412_cerebellum 0 .00 RPM 41 .81 RPM
SRP007412_heart 0 .03 RPM 54 .82 RPM
SRP007412_kidney 0 .08 RPM 51 .34 RPM
SRP007412_liver 0 .05 RPM 63 .74 RPM
SRP007412_testis 0 .00 RPM 121 .39 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_24 was not detected
15 EST(s) were mapped to retro_mmus_24 retrocopy
EST ID Start End Identity Match Mis-match Score
AA118417 72309297 72309732 99.1 431 4 427
AI787755 72309553 72309741 100 188 0 188
AV044672 72309584 72309818 95.8 224 10 214
BQ256447 72309217 72309885 100 668 0 668
BQ558855 72309658 72310061 100 403 0 403
BU559782 72309217 72309740 99.7 521 2 519
CA531941 72309658 72310228 100 570 0 570
CA949164 72309464 72309919 100 455 0 455
CD550387 72309228 72309740 100 512 0 512
CD550404 72309228 72309808 100 518 0 517
CD555716 72309219 72309736 100 517 0 517
CF172634 72309217 72309890 100 673 0 673
CF913648 72309217 72309853 100 636 0 636
CJ186546 72309200 72309808 100 432 0 430
CN691083 72309219 72309769 100 550 0 550
No TSS is located nearby retro_mmus_24 retrocopy 5' end.
retro_mmus_24 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_24 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Macaca mulatta ENSMMUG000000048021 retrocopy
Mus musculus ENSMUSG00000019977 1 retrocopy
retro_mmus_24 ,
Mus musculus ENSMUSG000000622031 retrocopy





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