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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttatgtgatagctatggatcatcaagattttaattgcaatgcttcttttcaaaactgaaagcagaaagggcataggagtttggacagatattctcgtttccgttttccttaaattttttattcaatctctccctcatatttcttaaatgtcctag

Basic information

species Zea mays
transcript GRMZM2G073950_T01
intron # 2
splice site 5'
intron type U2

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|211074743|gb|FL419972.1|FL419972
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|211141684|gb|FL053512.1|FL053512
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|91056600|gb|EB167018.1|EB167018
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|148953399|gb|EE152896.2|EE152896
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|78081735|gb|DV510147.1|DV510147
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|88758160|gb|DY542301.1|DY542301
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|50324199|gb|CO519325.1|CO519325
EST:     GTTGACTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|148939361|gb|EC883888.2|EC883888
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|78078908|gb|DV507320.1|DV507320
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|29167916|gb|CB411176.1|CB411176
EST:     G-TGATTAGAGAAGCACACAAGAAAGG-GCAAAGA-TGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|71417127|gb|DR803933.1|DR803933
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|211482279|gb|FL401962.1|FL401962
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|94478259|gb|EB707217.1|EB707217
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
EST: gi|78077686|gb|DV506120.1|DV506120
EST:     GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG                         GAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT
genomic: GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 220

GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttat ... aatgtcctagGAATTGTTTGAGGGGCACTATTTCTGCCAAGCTCAAAGACTGGATTTCTTTCGGCGCGCTAAGCCTTACAAAGGCAATCCAACTATTATAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAGgtaaatttatgtgatagctatggatcatcaagattttaattgcaatgcttcttttcaaaactgaaagcagaaagggcataggagtttggacagatattctcgtttccgttttccttaaattttttattcaatctctccctcatatttcttaaatgtcctag

- - - -  AGAAGC
- - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - GCAAAG