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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatttgctcgatggactctaaatgattagtaaacgttaggatgtttccataatcgttgatgtcttttcgtcttctaataatgcttcttttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG

Basic information

species Zea mays
transcript GRMZM2G094978_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 3'ss of exon 6
taaatttgctcgatggactctaaatgattagtaaacgttaggatgtttccataatcgttgatgtcttttc-gtcttctaataatgcttctttt--acatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG
 ||  ||  ||||   |   |  ||  || ||||    ||  || |||    |    || ||   ||||| || | |||| |    || | ||  | ||  || ||||||||| |||||||||||||||||||||| ||||| || |||||||| || ||||||||||||||||||||||||||
-aagctttgtcgacatatgatgtat--tttgtaataaataccatttttatcaacagtttaatagtttttcagtttactaacaccttttttcttggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG
















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|211136606|gb|FL156037.1|FL156037
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAAGCGGCAAAAGCTG
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCA-GCGGCAAAAGCTG
EST: gi|91056651|gb|EB167069.1|EB167069
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGAACTATAGG
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGG
EST: gi|88753379|gb|DY537520.1|DY537520
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|86467368|gb|DY233738.1|DY233738
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|13388479|gb|BG462185.1|BG462185
EST:     CAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: CAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|86470646|gb|DY237016.1|DY237016
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|13558959|gb|BG550314.1|BG550314
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|211329033|gb|FL456230.1|FL456230
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71764323|gb|DR962260.1|DR962260
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTTGT-ATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTG
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTT-GTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTG
EST: gi|16379404|gb|BI992921.1|BI992921
EST:     TTGGAGTTGATCCCCAAAG                         CTGTGTTGTTATTGAAGNCAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: TTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|101388001|gb|EB816015.1|EB816015
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|10697624|gb|BE997348.1|BE997348
EST:     GCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGCCAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|93011639|gb|EB637159.1|EB637159
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGG
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|60352425|gb|DN219398.1|DN219398
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71766391|gb|DR964328.1|DR964328
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|101382873|gb|EB813490.1|EB813490
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|60357150|gb|DN224123.1|DN224123
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71448345|gb|DR829395.1|DR829395
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71300530|gb|DR786320.1|DR786320
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|50327117|gb|CO522243.1|CO522243
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|101388003|gb|EB816016.1|EB816016
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
EST: gi|71766392|gb|DR964329.1|DR964329
EST:     GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG                         CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC
genomic: GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGC

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), 47 (downstream exon)
Score: 55

GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 433

GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG


Block sizes: 43 (upstream exon), 44 (downstream exon)
Score: 9

GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 110

GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGgtattgaaag ... ttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccataatcgttgatgtcttttcgtcttctaataatgcttcttttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG
                            ttctaat  putative branch site (score: 110)
                                     tgcttctttt  putative PPT
                            ttctaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaatttgctcgatggactctaaatgattagtaaacgttaggatgtttccataatcgttgatgtcttttcgtcttctaataatgcttcttttacatgcagCTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC