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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggataaaagtgtgtttcacgttttgtcatttttttatagatattagctattgctttatacatactagctacttttttgtacgtattatctaaatgtgctaaatagacaaaacctacttgtttccagttctaatgccatgtctgaacaatattgtatttttaaaaaaaatttatgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG

Basic information

species Zea mays
transcript GRMZM2G135283_T04
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 12
gtaggataaaagtgtgtttcacgttttgtcatttttttatagatattagctattgctttatacatactagctacttttttgtacgtattatctaaatgtgctaaatagacaaa---acctacttgtttccagttctaatgccatgtctgaacaat-attgtatttttaaaaaaaatttatgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG
                                                                                     |  || |||||||||||    ||| |||      |  || |||| | || | ||||||| |  | ||||| ||  |  | || |||     ||   | | ||||| |||||||||||||| |||||||||||||||||||  ||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||
-----------------------------------------------------------------------------------aatgatagctaaatgtgctttgcagataaacttgtttttttttttcaaatttttatgccatatggggacaattatcatcctcttcaaa-----tttcatgtttagGGCATAGATGGTTCAAGAGTGGAGAAGGTTTTAGAAAACGTGCACATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTACCAGGAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 12
gtaggataaaagtgtgtttcacgttttgtcatttttttatagatattagctattgctttatacatactagctacttttttgtacgtattatctaaatgtgctaaatagacaaaacctacttgtttccagttctaatgccatgtctgaacaatattgtatttttaaaaaaaatttatgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG
                                                                              |   | || | || |   ||| ||    |    |     |  || ||  | |    |    |    || | ||||||  || ||  ||||    || ||     |||| |||||||| ||||| ||||| || || ||||||   || |||||||||||||||||||| || ||||||||||||||||| || ||||| || || |
------------------------------------------------------------------------------taaaatgtttaatttt--tgtactgttaaccttagtaggaagtgcttagaatagctaatttactcttgtaaaatatttgatgttggaaaatgggttttg----cagGGAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCCTGGTGATGTTTCTGCCATGGTTCCCGGTG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 12
gtaggataaaagtgtgtttcacgttttgtcatttttttatagatattagctattgctttatacatactagctacttttttgtacgtattatctaaatgtgctaaatagacaaaacctacttgtttc---cagttctaatgccatgtctgaacaatattgtatttttaaaaaaaatttatgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG
                                                                                      ||     | |  || |   |  |   ||  ||  ||| ||    || | | ||   |     ||| |      ||||| | |  |   ||| | | |  |||| || ||||| || || || || ||||| || |||  ||| ||||||||||| ||||||||||| |||||||| ||||| || || ||||| || || |
------------------------------------------------------------------------------------aaatagataagagttgttggctccatttaatttatgtgtatcatttagcttttattataaaaaggaagagc-cactatttcttatga--ttttctctgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTGGAATCTGTTCATATTGCAGCTAACAAGAACACCGTTCCTGGAGATGTGTCGGCCATGGTTCCTGGTG

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|71299009|gb|DR785497.1|DR785497
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|67042253|gb|CO468508.1|CO468508
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|108953686|gb|EC364842.1|EC364842
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|113703934|gb|EE681438.1|EE681438
EST:     GGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: GGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|148945830|gb|EC891119.2|EC891119
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGATTCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|60353152|gb|DN220125.1|DN220125
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|14204327|gb|BG838004.1|BG838004
EST:     TCTCCGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|5804699|gb|AI979669.1|AI979669
EST:     TCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|6194529|gb|AW146633.1|AW146633
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|148928192|gb|EE284698.2|EE284698
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTTTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|148973318|gb|EE024403.2|EE024403
EST:     TTTCTGGTGGGACTGACAACCATTTAGTTTTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|60397906|gb|DN230722.1|DN230722
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|40336482|gb|CK370552.1|CK370552
EST:     TCTCCGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|148958251|gb|EC904465.2|EC904465
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTTTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|67024112|gb|CO452861.1|CO452861
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAAGGTTT-ANAAAGTGTGCATATTGC
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAA-GGTTTTAGAAAGTGTGCATATTGC
EST: gi|6102053|gb|AW126523.1|AW126523
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAAGGTTT-ANAAAGTGTGCATATTGC
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAA-GGTTTTAGAAAGTGTGCATATTGC
EST: gi|149089956|gb|EE179245.2|EE179245
EST:     ACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: ACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|60344488|gb|DN211461.1|DN211461
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|60343439|gb|DN210412.1|DN210412
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|37393418|gb|CF633973.1|CF633973
EST:     TCTCCGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|60357206|gb|DN224179.1|DN224179
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|89249961|gb|DY621747.1|DY621747
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|60352787|gb|DN219760.1|DN219760
EST:     TTCTGGTGGGAATGACAAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: CTCTGGTGGGACTGAC-AACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|113700941|gb|EE678445.1|EE678445
EST:     TCTCCGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTATAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|67013913|gb|CO442662.1|CO442662
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|60354435|gb|DN221408.1|DN221408
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
EST: gi|60349820|gb|DN216793.1|DN216793
EST:     TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG                         GGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA
genomic: TCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCA

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: 316

AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 367

AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 487

AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 456

AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaa ... atgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaatgccatgtctgaacaatattgtatttttaaaaaaaatttatgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG
 ttctaat  putative branch site (score: 456)
               tgaacaatattgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggataaaagtgtgtttcacgttttgtcatttttttatagatattagctattgctttatacatactagctacttttttgtacgtattatctaaatgtgctaaatagacaaaacctacttgtttccagttctaatgccatgtctgaacaatattgtatttttaaaaaaaatttatgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT