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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttttgacaacccttagctgcatagctcattgtttccagttgatgacattttttctgaatagaaagtaactatattcagtttatattttgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGCGAATTTGATTTGGAGAAT

Basic information

species Zea mays
transcript GRMZM2G020446_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 1
tggttttgacaacccttagctgca-tagctcattgtttccagttgatgacatttt-ttctgaatagaa----agtaacta--tattcagtttatattttgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGCGAATTTGATTTGGAGAAT
        | |  | ||| ||| |  |  | | |  ||| |||| ||| || ||  | |  || | ||    ||||||||  || |     ||| | || ||| ||||||| |||||||| |||||||| |||||| | ||| |||||   |||||||| ||||| ||||| ||||||||  | || || ||||||||||||||||||
-------taaagtctttatctgtaacaaataagtacttc-agttcatgtcaattgataccaaacaaaattgtagtaactaactagtttaagtatttatttaagttcagGTGTATATTTAATGGAAATGGAAAGACATTGGAAGATCTTGTTTTAGCTGCAGAGAGCGGAGTGTTTGTAAACATAGACAGTGAATTTGATTTGGAGAAT
















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|211008643|gb|FL282358.1|FL282358
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAA
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAA
EST: gi|211008647|gb|FL282362.1|FL282362
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGGAAATGGGAAGACACTCGAAGATCCTTAA-TTAGCT
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGG-AAATGGGAAGACACTCGAACATC-TTAAATTAGCT
EST: gi|211005873|gb|FL282350.1|FL282350
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGGACATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|148934359|gb|EC878388.2|EC878388
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|211003081|gb|FL282330.1|FL282330
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|211008652|gb|FL282367.1|FL282367
EST:     CGGCAACGAGCTCCGACTCGNCCCTC-AGGCGGGATTTCGACCC-GCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTA
genomic: CGGCAACGAGCTCCGACTCG-CCCTCCAGGCGGGATT-CGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTA
EST: gi|211008642|gb|FL282357.1|FL282357
EST:     AGCGGAAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GGGCATATTTAACGGAAATGGGGAAAACACTCGAACATCTTAAATTAACTG
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGG-AAGACACTCGAACATCTTAAATTAGCTG
EST: gi|211011420|gb|FL282372.1|FL282372
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|76928257|gb|DV171542.1|DV171542
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|211003080|gb|FL282329.1|FL282329
EST:     GCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCCGC-AG                         GTGTATATTTAA
genomic: GCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCC-GCCAGgtgcggttct ... tgaagatcagGTGCATATTTAA
EST: gi|211003087|gb|FL282336.1|FL282336
EST:     GCGGCTACGAGCTCCGACTCCCCCTTCCAG-CGGGATTCGACCCCGCC-G                         GTGGCATATT-AACGGGAAATGGGAAGACACTC
genomic: GCGGCAACGAGCTCCGACTCGCCCT-CCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTG-CATATTTAACGG-AAATGGGAAGACACTC
EST: gi|211005870|gb|FL282347.1|FL282347
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTTACGGANATGGGAAGACACTCGAACATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|211008641|gb|FL282356.1|FL282356
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGTCAG                         GTGTATATTTAACGGAAATGGCGA-GACACTCGAA
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGG-GAAGACACTCGAA
EST: gi|211008644|gb|FL282359.1|FL282359
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTANATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|22545814|gb|BU098188.1|BU098188
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GGGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|211008645|gb|FL282360.1|FL282360
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACATCT-AAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|50329919|gb|CO525045.1|CO525045
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|211003079|gb|FL282328.1|FL282328
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|211003083|gb|FL282332.1|FL282332
EST:     GCGGCAACGAGCTCCGACTCGCC-TCCCAGGCGGGATTCGACCCCGCCAG                         GGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTA
genomic: GCGGCAACGAGCTCCGACTCGCCCTCC-AGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagG-TGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTA
EST: gi|211005867|gb|FL282344.1|FL282344
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATT
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATT
EST: gi|9825116|gb|BE575318.1|BE575318
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|26457088|gb|CA828671.1|CA828671
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|20811294|gb|BQ295772.1|BQ295772
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|211376700|gb|FL282323.1|FL282323
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGGAGACACTCGAACATCTTAAATTAGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGC
EST: gi|211003085|gb|FL282334.1|FL282334
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTA
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTA
EST: gi|211003086|gb|FL282335.1|FL282335
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTCGAACAT
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACAT
EST: gi|211008640|gb|FL282355.1|FL282355
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGCATATTTAACGGAAATGGGAAGACACTC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTC

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: 150

TCCCCGTGCTACGCGTCCTGCGTGAGCTTGGCTGCGGCGCCGTCCTCGTCAGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGCGAATTTGATTTGGAGAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 122

TCCCCGTGCTACGCGTCCTGCGTGAGCTTGGCTGCGGCGCCGTCCTCGTCAGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGCGAATTTGATTTGGAGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

TCCCCGTGCTACGCGTCCTGCGTGAGCTTGGCTGCGGCGCCGTCCTCGTCAGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGCGAATTTGATTTGGAGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

TCCCCGTGCTACGCGTCCTGCGTGAGCTTGGCTGCGGCGCCGTCCTCGTCAGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggttct ... tgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGCGAATTTGATTTGGAGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacattttttctgaatagaaagtaactatattcagtttatattttgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGCGAATTTGATTTGGAGAAT
                    aagtaac  putative branch site (score: 90)
                   aaagtaactatattca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggttttgacaacccttagctgcatagctcattgtttccagttgatgacattttttctgaatagaaagtaactatattcagtttatattttgaagatcagGTGCATATTTAACGGAAATGGGAAGACACTCGAACATCTTAAATTAGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGCGAATTTGATTTGGAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - gctgcat
- - - - - - - - - - - - - - - - - - - - gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatagaaa