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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgagttcccaacctgccagcatgtcttgttttttcttgaactcagttggttacactgctgccttagcatacataatgctaaggagatagtaagc...

Basic information

species Zea mays
transcript GRMZM2G113742_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113742_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g25799.1 (Oryza sativa), 5'ss of exon 5
GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgagttcccaacctgccagcatgtcttgttttttcttgaactcagttggttacactgctgccttagc-atacataatgctaaggagatagtaagc--
|||||||||| | |||||||||||||||||||| |||||||||||||||| |||||| ||||||||||||||||    ||||  |   ||   |     ||    | ||     ||  |||||    | |    |   || |    | ||| | || ||    |   |  |  
GAGTCAAGAACTAAAAGAAGCACTCAGAGCACAGATGGAAGTGCAACGAAAATTGCATGAACAAGTGGAGgtaagtaaagttttc--tctaaaatggcatcagcatgttgaaataagacagttcaccaaatgcttctttttgttgcaaatagttctgagttc-tgacattcct
















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|78087009|gb|DV515402.1|DV515402
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|9733589|gb|BE512341.1|BE512341
EST:     CAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|60345818|gb|DN212791.1|DN212791
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|76916796|gb|DV166557.1|DV166557
EST:     CACTCAGAGCACAAAGGGAAGGGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|211108289|gb|FL269572.1|FL269572
EST:     ACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAAACA-GTGGAG                         GTCCAGAAGCATATGCAGATCCGA
genomic: ACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAA-CAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGA
EST: gi|24773354|gb|CA408608.1|CA408608
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|211222683|gb|FL110211.1|FL110211
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|24961617|gb|CA483617.1|CA483617
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|101389911|gb|EB816886.1|EB816886
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|76909193|gb|DV163265.1|DV163265
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|88757895|gb|DY542036.1|DY542036
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|78073924|gb|DV502358.1|DV502358
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|71426738|gb|DR807788.1|DR807788
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|30087487|gb|CB885693.1|CB885693
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|149007848|gb|EE040277.2|EE040277
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|211222684|gb|FL110212.1|FL110212
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|60341005|gb|DN207978.1|DN207978
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|76932640|gb|DV173098.1|DV173098
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|211222687|gb|FL110215.1|FL110215
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|211222685|gb|FL110213.1|FL110213
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|74240765|gb|DT648679.1|DT648679
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|9731208|gb|BE509960.1|BE509960
EST:     CACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|101386138|gb|EB815112.1|EB815112
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|71318298|gb|DR795913.1|DR795913
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|211222686|gb|FL110214.1|FL110214
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|67026619|gb|CO455368.1|CO455368
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|101389909|gb|EB816885.1|EB816885
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|78120958|gb|DV539342.1|DV539342
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|76932639|gb|DV173097.1|DV173097
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|60341894|gb|DN208867.1|DN208867
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|30087488|gb|CB885694.1|CB885694
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCA
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCA
EST: gi|60400474|gb|DN233281.1|DN233281
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|76916798|gb|DV166558.1|DV166558
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
EST: gi|149007847|gb|EE040276.2|EE040276
EST:     CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAG                         GTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC
genomic: CACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGAC

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: 46 (upstream exon), 48 (downstream exon)
Score: 87

GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGACACGATACTAGATAAGGCGTTCAAGATAGTATCTGAGCAACTGAGTGGCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 53

GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGACACGATACTAGATAAGGCGTTCAAGATAGTATCTGAGCAACTGAGTGGCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 63

GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGACACGATACTAGATAAGGCGTTCAAGATAGTATCTGAGCAACTGAGTGGCT


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 23

GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgag ... catttattagGTCCAGAAGCATATGCAGATCCGAATGGAGGCGAACCAGAAGTACATCGACACGATACTAGATAAGGCGTTCAAGATAGTATCTGAGCAACTGAGTGGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAGATTGCACGAACAAGTGGAGgtaacatgagttcccaacctgccagcatgtcttgttttttcttgaactcagttggttacactgctgccttagcatacataatgctaaggagatagtaagc

- - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG