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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttataaataattacattctgtgttttagaacctattttcctggtcactgagttcatactcatcaattattatgatgtggtgtcaacactaacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG

Basic information

species Zea mays
transcript GRMZM2G365035_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G365035_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 8
tgttataa-ataattacattctgtgttttagaacctattttcctggtcactgagt--tcatactcatcaattattatgatgtggtgtcaacactaacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG
   ||| | ||    |  ||| |   | |  |   | |    |   | | | |||  ||   || || |  ||| |  || || ||||||||||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  |||| || 
--atatgacatgcggaacttcggcagtgtcaattttttacctcacatta-taagtcatctgtcttattagctatcactatatgatgtcaacactaatttgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATTGTTGAGGCA
















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|149087834|gb|EE287144.2|EE287144
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|211142539|gb|FL467000.1|FL467000
EST:     CATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|32840606|gb|CD980287.1|CD980287
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|76017952|gb|DT945122.1|DT945122
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|149043308|gb|EE047371.2|EE047371
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|60345110|gb|DN212083.1|DN212083
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|22489585|gb|BU049508.1|BU049508
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|211516679|gb|FL422119.1|FL422119
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|76284446|gb|DV024014.1|DV024014
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|87153749|gb|DY398538.1|DY398538
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|32935092|gb|CF039904.1|CF039904
EST:     CCATTGATGTTGCCAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|18384244|gb|BM417443.1|BM417443
EST:     CGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|37388728|gb|CF631576.1|CF631576
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|33091766|gb|CF051760.1|CF051760
EST:     CCATTGATGTTGACAAAAATGGAACGATTGGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|22489749|gb|BU049672.1|BU049672
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|32840607|gb|CD980288.1|CD980288
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|45567561|gb|CK985631.1|CK985631
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
EST: gi|149102041|gb|EE188040.2|EE188040
EST:     CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAG                         GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG
genomic: CCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAG

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: 45 (upstream exon), 42 (downstream exon)
Score: 160

ATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAATTCAATGCCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 257

ATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAATTCAATGCCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 395

ATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAATTCAATGCCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 192

ATCTACATTAAACTCAGAAGAGATGTCTGATCTTCGTGATCAATTCAATGCCATTGATGTTGACAAAAATGGAACGATTAGTCTTGAGGAACTGAAGCAGgtaaactatg ... taacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactgagttcatactcatcaattattatgatgtggtgtcaacactaacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG
                                          cactaac  putative branch site (score: 192)
                 atcaattattatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttataaataattacattctgtgttttagaacctattttcctggtcactgagttcatactcatcaattattatgatgtggtgtcaacactaacgtgcagGCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - ttcctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg