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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtccccccttgtgtttgtctagctatatatgatttttttaacattagtatgcttgatcaaag

Basic information

species Zea mays
transcript GRMZM2G080652_T01
intron # 4
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|101391113|gb|EB817490.1|EB817490
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTC
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTC
EST: gi|211040785|gb|FL108285.1|FL108285
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|32837961|gb|CD977639.1|CD977639
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGGGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|32823725|gb|CD963447.1|CD963447
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|31360794|gb|CD445151.1|CD445151
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|78117501|gb|DV535888.1|DV535888
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCTAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|71330852|gb|DR802224.1|DR802224
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|32823775|gb|CD963497.1|CD963497
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGAATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|76294373|gb|DV033941.1|DV033941
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|24768059|gb|CA403191.1|CA403191
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|61119643|gb|DN560604.1|DN560604
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|78117500|gb|DV535887.1|DV535887
EST:     CGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: CGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|71330843|gb|DR802223.1|DR802223
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|101386958|gb|EB815496.1|EB815496
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
EST: gi|71309454|gb|DR791014.1|DR791014
EST:     TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT
genomic: TCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCT

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: 79

AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 66

AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtcc ... ttgatcaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAGgtaagtgtccccccttgtgtttgtctagctatatatgatttttttaacattagtatgcttgatcaaag

- - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - -  AGATCA