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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatatagttaaatatttagatatttttcatagtttgacatgtgcctgtcaattattcatccaataattaaactggtattgaccattggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG

Basic information

species Zea mays
transcript GRMZM5G815009_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g59440.2 (Oryza sativa), 3'ss of exon 2
tgatatagttaaatatttagatatttttcatagtttgacatgtgcctgtcaattattcatccaata---attaa--------actggtattgaccattggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG
            || | | ||  ||||   |||||| |  | ||  ||| | ||||||    |||    ||| |          | ||||| |||||  ||| || || ||||| || |||||||| |  ||||||||||| ||||| || || |||||||||||||||||||| |||||||||||| ||||||||||||||||||| |||
-----------gatgtattgaagttttgtttagtttaatgtatgattgttagttattcgcataatttatattgatgcactttggtagtattaaccatcagcattggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAATTTGAAGAATCTTATAAGCTTGGACCTGTACAAGAACAACATTTCTGGG

upper sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G44250.2 (Glycine max), 3'ss of exon 2
tgata-tagttaaatatttagatatttttcatagtttgacatgtgcctgtcaattattcatccaataat-taaactggtattgaccattggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG
|  || ||  |   ||||| | | |   ||     |||   ||  |      |||    | |   || | |  | ||   ||  |  ||      ||  ||| ||  | ||||| |||| |||||||||||| || ||| | || ||||| ||  |||||| |||| | ||||||||||||||||| |||||||| || || 
tattactaaattggtattt-gctgtggctctcttattgttgtgaactatagcatttcatacctgttagtgtttaatgaggttttctttttat-tggatgtagTGAGTTGTACAAAAACAACATTCAAGGAACTATTCCTCCGGAACTTGGAAACCTGAAGAGTCTAGTTAGCTTGGACTTGTACAACAACAACATATCAGGC

upper sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G04520.1 (Glycine max), 3'ss of exon 2
---tgatatagttaaatatttagatatttttcatagtttgacatgtgcctgtcaattattcatccaataat-taaactggtattgaccattggcactgaa-atagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG
   ||||    ||     |||   |   | || ||  |||   ||  |     |||| |  | |   || | |  | ||   ||  |  ||  || || |  ||| ||  | ||||| |||| |||||||||||| || ||| | || ||||| ||  |||||| |||  | ||||||||||||||||| |||||||| || || 
gattgat-cgattggtattttctgtggctctctta--ttgttgtgaactatagaattttatacctgttagtgtttaatgtggttttctttt--cattggatgtagTGAGTTGTACAAAAACAACATTCAAGGAACTATTCCTCCAGAACTTGGAAACCTGAAGAGTCTCGTTAGCTTGGACTTGTACAACAACAACATATCAGGC

upper sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G43740.1 (Arabidopsis thaliana), 3'ss of exon 2
tgatatagttaaatatttagatatttttcatagtttgacatgtgcctgtcaattattcatccaataattaaactggtattgaccattggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG
         ||   | | |    | |||     |||||           || |||      || | |   |  |   |||   | |||  | | | |||| ||||| ||||| |||   ||||||||||| || |||||||||||||| ||| |||||| |||||| || |||||  ||||||| |||||  |  | |||
--------gtatggaatcatcactcttttgccttttgattatctgaaaacatttacattatcagtcacacatataacattttgctttg--agtcatatagTGAACTCTACAAAAACGAGATTCAAGGAACTATACCTTCTGAGCTTGGAAATCTGAAGAGTCTAATCAGTTTGGATCTGTACAACAACAATCTCACCGGG

upper sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0040g00520.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------------------tgatatagttaaatatttagatattt-ttcatagtttgacatgtgcct-gtcaattattcatccaataattaaactggtattgacc--attggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG
                                                                         ||  | ||||   ||| |  | | || || ||    ||  ||||     |   || |||||       |   || ||  ||| |    | |    || |   || || ||||||||||||| ||||||||| |||||||||  ||||||||| || || ||||| ||||| |||||||| |||||||| |||||||| ||||||
gtaagtgtcttttaatttgctgttaaaatttgccaataacgagtgcgttgcttggtgtcaaatgttagctttatgtaagagttctctatctgaacaattgttgatgtcatgtgatgtttggagcttataattcaaagccacagggaaatgaaattaaattaagttcttctcatgcagAGAGCTTTACAAGAACAACATTCAAGGGACAATCCCTGTTGAGCTTGGAAACTTAAAGAACCTAATCAGCTTGGATTTGTACAACAACAACATCTCGGGG

upper sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0009g01210.t01 (Vitis vinifera), 3'ss of exon 2
-tgatatagttaaatatttagatatttttcatagtttgacatgtgcc-tgtcaattattcatccaataattaaactggtattgaccattggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG
     ||  ||  || | | || |    |   |     | ||||||   |    ||||| || |    ||   | |  ||||     |      | |  |||||| |||||||| |||  |||||||||||| ||||||  ||||||||| ||||||| ||  ||||| ||||||||||| || |  |||||||| || |||
tcagcatttttccatgtgttgacaggagtgcaatgcaaaaatgtgctgcggattttattaattcttagatattatt--tattctttttcactcttcatgtagGGAGCTTTACAAAAACCACATTCAAGGAACTATCCCTGTTGAGCTTGGCAATTTGAGGAGCCTAATCAGCTTGGACTTATATAGCAACAACATCTCAGGG

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|211004213|gb|FL095607.1|FL095607
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTT
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTT
EST: gi|149104284|gb|EE289722.2|EE289722
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|211004214|gb|FL095608.1|FL095608
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGCAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTN
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGG-AACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTA
EST: gi|89756077|gb|DY686250.1|DY686250
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|211004206|gb|FL095600.1|FL095600
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|211004205|gb|FL095599.1|FL095599
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGC
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGC
EST: gi|211396372|gb|FL095576.1|FL095576
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTTGGYT
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTT-GG-T
EST: gi|211004211|gb|FL095605.1|FL095605
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|93284383|gb|EB676647.1|EB676647
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|211001434|gb|FL095594.1|FL095594
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGT
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGT
EST: gi|89249279|gb|DY621065.1|DY621065
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCCTTCTGAGCTTGGTA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCC-TTCTGAGCTTGGTA
EST: gi|91054725|gb|EB165143.1|EB165143
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|91051618|gb|EB162036.1|EB162036
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|211004209|gb|FL095603.1|FL095603
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|149101778|gb|EE287382.2|EE287382
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|50336224|gb|CO531350.1|CO531350
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|211004201|gb|FL095595.1|FL095595
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|149106063|gb|EE291719.2|EE291719
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|148933095|gb|EC876727.2|EC876727
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|211001424|gb|FL095584.1|FL095584
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|211001428|gb|FL095588.1|FL095588
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
EST: gi|74240378|gb|DT648292.1|DT648292
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT                         GGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaagttctt ... actgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtcaattattcatccaataattaaactggtattgaccattggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG
                               tattgac  putative branch site (score: 2)
     aattattcatccaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatatagttaaatatttagatatttttcatagtttgacatgtgcctgtcaattattcatccaataattaaactggtattgaccattggcactgaaatagGGAACTTTACAAGAACAGCATTCAAGGAACAATCCCTTCTGAGCTTGGTAATTTGAAGAATCTAATAAGCTTGGACTTGTACAAGAACAACATTTCGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - -tgacatg
- - - - - - - - - - - - - - - - - - - - - tgcctgt