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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATATGCCACTGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTAGTAAGAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaacttgataatattctctttatttttgtttatcaaccgttgtccttcatgcagtgatgatcttctctgaattttcag

Basic information

species Oryza sativa
transcript LOC_Os08g39070.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g39070.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 7
TGATATGCCACTGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTAGTAAGAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaacttga--taatattct--------ctttatttttgtttatcaaccgttgtccttcatgcagtgatgatcttctctgaattttcag-------------------------------------------------------------------------------------------------
||| || ||| |||||||||||||||||||||||||||||||||| |||||||||||||| || | ||| ||| | |||||||||||||||||  ||||||| ||||   || |  |   ||  |           | | |   || ||  |    | |  |||||    |||  |  || | |||  |  |||                                                                                                 
TGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAAGAAGGCTACCGGCTACGGAATCACAGAAATTCCAAGATGACTTTTTAATGgtatgctcgtttcacttctcatcttggacagagtgctctctcatttgatatagaaatatatttcattatatgaatacattatttgacataccagctatattgccagtaaagctcgactttctgtacttttcccatggctgtatatttaaccctatatgtgtaattatgacggtgccattcgttcttaacag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|87024597|gb|CI259312.1|CI259312
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|86256930|gb|CI061693.1|CI061693
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|87035572|gb|CI190194.1|CI190194
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|58600992|gb|CK011520.1|CK011520
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|16578082|gb|BI812177.1|BI812177
EST:     TCCAAGATGACTTCCTAATG                         GAATACACATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTG
genomic: TCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACA-ATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTG
EST: gi|58677484|gb|CK066171.1|CK066171
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|86603350|gb|CI112110.1|CI112110
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|88964490|gb|CI055186.1|CI055186
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|88490846|gb|CI428118.1|CI428118
EST:     CAGCAATGGAGTCAGAGAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: CAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|88960516|gb|CI006477.1|CI006477
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|18385597|gb|BM418796.1|BM418796
EST:     GAAGGCTACCAGCAATGGAGTCAG-AAAATTCCAAGATGACTTCCTAATG                         GAATACANATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTG
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACA-ATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTG
EST: gi|86599885|gb|CI256047.1|CI256047
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|88201787|gb|CI202142.1|CI202142
EST:     AAGGCTACCAGCAATGGAGTCAGAGAAATTCCAAGATGACTTCGCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTG
genomic: AAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTC-CTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTG
EST: gi|86593400|gb|CI258040.1|CI258040
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|87035583|gb|CI190205.1|CI190205
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|16578081|gb|BI812176.1|BI812176
EST:     TCCAAGATGACTTCCTAATG                         GAATACCATGACACCCTCCTCATGACTTACCTTGCTATGTTCCCTAACTGT
genomic: TCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|86251601|gb|CI016890.1|CI016890
EST:     GAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
EST: gi|27546787|gb|CA764823.2|CA764823
EST:     GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATG                         GAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT
genomic: GAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 60 (downstream exon)
Score: 24

TGATATGCCACTGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTAGTAAGAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaac ... gaattttcagGAATACAATGACACCCTCCTCATGACTTACCTTGCTATGTTCACTAACTGTTCAAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATATGCCACTGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTAGTAAGAAGGCTACCAGCAATGGAGTCAGAAAAATTCCAAGATGACTTCCTAATGgtctgctaacttgataatattctctttatttttgtttatcaaccgttgtccttcatgcagtgatgatcttctctgaattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG