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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgctttgtcttgaacctgagcttacaatatggttcatattggtgaatcttttgattgtctaatcttcattgttctcttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA

Basic information

species Oryza sativa
transcript LOC_Os02g41590.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 3
------------gtaacgc-tttgtcttgaacctgagcttacaatatggttcatattggtgaatcttttgattgtcta-atcttcattgttct----cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
             ||||   ||| |   | |    ||   |  |  || | ||  ||||||| || | |||| || |  ||||||||| || |    ||| |  ||||||||||||||||||||||||||||||| |||
gtaatgtttcttataacatgtttatgcagtattgcagtccatgaattgttacaacttggtgactcctctgatggtttgtatcttcattctttttattcttatcacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 3
------------gtaacgctt-tgtcttgaacctgagcttacaatatggttcatattggtgaatcttttgattgtcta-atcttcattgttct----cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
             ||||   | | |   | |     |   | ||  |  | |   ||||||| |||| |||| || |  |||||  || || |    ||| || ||||||||||||||||||||||||||||||| |||
gtaatgtttcttataacttgtatatgcagtattgctgtccataaattattacgacttggtgactcttctgatggtttgtatctttgttctttttattcttattacagGAGCCACCCAGAACTCTATCAGGGTTGCCCAA
















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|84117280|gb|CD151047.1|CD151047
EST:     GTATGATGAGTTGGCCAGCAAGGGGGGTGTTGAATATATTGCCGGAG                         GAGCCACCCCCAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|27576661|gb|CA999355.1|CA999355
EST:     CAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: CAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|428330|gb|D24478.1|D24478
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|58598930|gb|CK009458.1|CK009458
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCCGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|163918496|gb|EG710298.1|EG710298
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|428228|gb|D24376.1|D24376
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|88719065|gb|CI742575.1|CI742575
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|88733084|gb|CI756261.1|CI756261
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|88394239|gb|CI603428.1|CI603428
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|66922324|gb|CX109172.1|CX109172
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|55410432|gb|CV722808.1|CV722808
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
EST: gi|58657974|gb|CK046654.1|CK046654
EST:     GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG                         GAGCCACCCAGAACTCTATCAGGGTTGCTCAA
genomic: GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA

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: 72 (upstream exon), 67 (downstream exon)
Score: 127

GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAGgtaacgcttt ... cttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttcatattggtgaatcttttgattgtctaatcttcattgttctcttcttccagGAGCCACCCAGAACTCTATCAGGGTTGCTCAA
                          gtctaat  putative branch site (score: 127)
                                tcttcattgttctctt  CT-rich tract
              aatctttt  TA-rich tract