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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGTTTCCGATGACTACTATACTGATGACGAGGATGATGGCGAGGAGGAACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagctacagagtatgctttgctggttgcagtgcgctgcttgattattcctgtactggccatatatgggctctctgctagtaactgctatccttca...

Basic information

species Zea mays
transcript GRMZM2G540403_T01
intron # 1
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|32923745|gb|CF028557.1|CF028557
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCCCCCCAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|110194732|gb|EC876630.1|EC876630
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCCCAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGGGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|148936722|gb|EC880854.2|EC880854
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCCCAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|71435936|gb|DR816986.1|DR816986
EST:     AAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: AAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|71762224|gb|DR960161.1|DR960161
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|148972198|gb|EE023075.2|EE023075
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|74233122|gb|DT641036.1|DT641036
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|71329156|gb|DR801289.1|DR801289
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|32938936|gb|CF043755.1|CF043755
EST:     ACTGGTCGAGCAAGAAGCAGAAGATGGTACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|149090708|gb|EE180041.2|EE180041
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGGGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|78108128|gb|DV526546.1|DV526546
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|76292665|gb|DV032233.1|DV032233
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|211023804|gb|FL455117.1|FL455117
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|32924288|gb|CF029100.1|CF029100
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCCCCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|13382188|gb|BG458863.1|BG458863
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
EST: gi|101381964|gb|EB813039.1|EB813039
EST:     ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAG                         ATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG
genomic: ACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAG

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: 48 (upstream exon), 43 (downstream exon)
Score: 61

AGTGTTTCCGATGACTACTATACTGATGACGAGGATGATGGCGAGGAGGAACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAGATTTGTTGTTTCGCATTTGTTATGTTACCCTCAGGTGAGGATGGTGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 463

AGTGTTTCCGATGACTACTATACTGATGACGAGGATGATGGCGAGGAGGAACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAGATTTGTTGTTTCGCATTTGTTATGTTACCCTCAGGTGAGGATGGTGGGG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 13

AGTGTTTCCGATGACTACTATACTGATGACGAGGATGATGGCGAGGAGGAACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAGATTTGTTGTTTCGCATTTGTTATGTTACCCTCAGGTGAGGATGGTGGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

AGTGTTTCCGATGACTACTATACTGATGACGAGGATGATGGCGAGGAGGAACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagct ... atattctcagATGCAACTGAAGAGGGCGAGGCAGACAGCAGCTCCTAGGCGGGAAGTGTAGATTTGTTGTTTCGCATTTGTTATGTTACCCTCAGGTGAGGATGGTGGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGTTTCCGATGACTACTATACTGATGACGAGGATGATGGCGAGGAGGAACTGGTCGAGCAAGAAGCAGAAGAAGGCACCACAGCAGATGCTGCTCCAGgtacatagctacagagtatgctttgctggttgcagtgcgctgcttgattattcctgtactggccatatatgggctctctgctagtaactgctatccttca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT