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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggctacaagaagtgatggtcgtgtgtgtattgtttctaatagtagtaggtaatatggtctctaatattctcccttttggtctacccaattatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAGGCCTCCCCAATCCGTTTGATTTTTCTTCTATGAGCAACTTGCTCAAT

Basic information

species Zea mays
transcript GRMZM5G800734_T02
intron # 1
splice site 3'
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|211076127|gb|FL369082.1|FL369082
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCTTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211269360|gb|FL417928.1|FL417928
EST:     GCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCA
genomic: GCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGC-AAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCA
EST: gi|211319046|gb|FL374772.1|FL374772
EST:     TCGCAGGCATCG-CCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|21809484|gb|BQ667802.1|BQ667802
EST:     GATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: GATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|213175660|gb|FM183110.1|FM183110
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|116823815|gb|EC867386.1|EC867386
EST:     CGCAGTGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: CGCAG-GCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|22546077|gb|BU098398.1|BU098398
EST:     TC-CAGGCATCTCCCTCTCGCCGGG-CGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211418388|gb|FL391640.1|FL391640
EST:     TCGCAAGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|20507180|gb|BQ279520.1|BQ279520
EST:     CCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: CCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211042826|gb|FL411665.1|FL411665
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCTTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|13316075|gb|BG410522.1|BG410522
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|31558362|gb|CD527574.1|CD527574
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|14242838|gb|BG840655.2|BG840655
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211062797|gb|FL382546.1|FL382546
EST:     TCGCAGGCATCG-CCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|91869881|gb|EB400588.1|EB400588
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211525125|gb|FL427343.1|FL427343
EST:     TCGCAGGCATCG-CCTCTCGCCGGGNCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211082181|gb|FL396892.1|FL396892
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|32860620|gb|CF000302.1|CF000302
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|19058108|gb|BM736775.1|BM736775
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|13316076|gb|BG410523.1|BG410523
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211387599|gb|FL400575.1|FL400575
EST:     TCGCAGGCATCG-CCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211051648|gb|FL410420.1|FL410420
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211490699|gb|FL394416.1|FL394416
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211050742|gb|FL374473.1|FL374473
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211322030|gb|FL425792.1|FL425792
EST:     TCGCAGGCATCG-CCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211494459|gb|FL428225.1|FL428225
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211377247|gb|FL413756.1|FL413756
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211014193|gb|FL395353.1|FL395353
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
EST: gi|211206607|gb|FL376335.1|FL376335
EST:     TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCG                         ATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG
genomic: TCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAG

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: 371

CGTTTTCCTCTCCGAGTCCTCCCTGGCCTCTCAACCACTCATCATCGCCTTCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAGGCCTCCCCAATCCGTTTGATTTTTCTTCTATGAGCAACTTGCTCAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 593

CGTTTTCCTCTCCGAGTCCTCCCTGGCCTCTCAACCACTCATCATCGCCTTCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAGGCCTCCCCAATCCGTTTGATTTTTCTTCTATGAGCAACTTGCTCAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 291

CGTTTTCCTCTCCGAGTCCTCCCTGGCCTCTCAACCACTCATCATCGCCTTCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAGGCCTCCCCAATCCGTTTGATTTTTCTTCTATGAGCAACTTGCTCAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 322

CGTTTTCCTCTCCGAGTCCTCCCTGGCCTCTCAACCACTCATCATCGCCTTCGCAGGCATCGCCCTCTCGCCGGGCCGTCCGATTCCGCCATGGCTTCCGgtatctgcta ... tatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAGGCCTCCCCAATCCGTTTGATTTTTCTTCTATGAGCAACTTGCTCAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggtaatatggtctctaatattctcccttttggtctacccaattatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAGGCCTCCCCAATCCGTTTGATTTTTCTTCTATGAGCAACTTGCTCAAT
              ctctaat  putative branch site (score: 322)
                                            ttatctttc  putative PPT
                                          aattatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggctacaagaagtgatggtcgtgtgtgtattgtttctaatagtagtaggtaatatggtctctaatattctcccttttggtctacccaattatctttcagATGAGAGCAAAAATTCAAAACCAGAGAAGCCATCTTCAGCAGCTGGTGCAGGCCTCCCCAATCCGTTTGATTTTTCTTCTATGAGCAACTTGCTCAAT

- gctacaa
- - - - - - -tgatggt
- - - - - - - - - - - - - - - -tgtttct