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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttctaggctatctgacatgcaatagaataaattccatggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC

Basic information

species Zea mays
transcript GRMZM2G000749_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 2
-------atgttctaggctatctgacatgcaatagaataaattccatggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
       ||||| | ||| |||||  ||| |||| || || |||   || |||     |  ||| || ||||   ||   ||     ||  | || |   ||||||||| ||  ||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || ||| |||| ||||| ||||| |
ttcattcatgttatgggc-atctgttatggaataaaacaacttctgaggcctt-gcagtgttaggaacttaagctttatttc---ggttcgtctgtt--gttttcagGTTGACTTGGAGCACAATCAATATAGGTCATTTCAGGGTTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAGGATTTTGTTGTAGACACCCTTAAAC

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
---atgttctaggctatctgac-atgcaatagaataaattcca---tggacttcatgatactagcaatttaatgattgcctctataatttttttgctcc--attttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
   |      |    |  | |   |||| ||   |  | |      |   |||| |||  |||  |  |     | |   | ||    ||  |   |    || || |||| ||| ||||||||||||||||| |  | || || |||||||| ||| ||||||| || |||||||| || ||||| |||||||| |||||| | || |
gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgac-ctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 3
----atgttctaggctatctgacatgcaataga---ataaattccatggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
    || |||    || |||   |  || |      || | ||||||  | | |||  |  |  |   || |||  |      || | ||         || |  |||| ||| |||| |||||||||||| |||| || || || ||||| ||| ||||||| ||||||||||| || ||||| |||||||| |||||  | || |
gctgatattcc--cctttcttgtagtcactccctccattacttccattcattgcattcttttgacttatttatgtata-----atgacttgaagttgaaatgtatagGTTGATTTGGAACATAATCAATATCGGTCTTTCCAAGGTTTGACTTGCCTGATGCAAATTTCAACAAGGACTGAAGATTTTATTGTTGACACATTGAAAC

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
atgttctaggctatctgacatgc-aatagaataaattcca--tggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
    |||     ||  || | || || | |||| |||| |  | || ||    || ||      |      |  | |   |  ||| |||   |  |||| |||| ||||||||||||||||| ||||| || ||||| || ||||| ||||||||||| ||||| || |||||||| || | ||| || || ||  ||||||
---ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC

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|211270555|gb|FL015563.1|FL015563
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211268121|gb|FL015554.1|FL015554
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211265687|gb|FL015541.1|FL015541
EST:     AGGCTTAACAGAATTAAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGGTCATTTTCAGGGCTTGACCTGCT
genomic: AGGCTTAACAGAATTA-GCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGG-TCATTT-CAGGGCTTGACCTGCT
EST: gi|211270558|gb|FL015566.1|FL015566
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211265690|gb|FL015544.1|FL015544
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211268118|gb|FL015551.1|FL015551
EST:     AAGGCTTAACAGAATTANCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211265688|gb|FL015542.1|FL015542
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211270568|gb|FL015576.1|FL015576
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|60338799|gb|DN205772.1|DN205772
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211270566|gb|FL015574.1|FL015574
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211270559|gb|FL015567.1|FL015567
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211268127|gb|FL015560.1|FL015560
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211270561|gb|FL015569.1|FL015569
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211265693|gb|FL015547.1|FL015547
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211270567|gb|FL015575.1|FL015575
EST:     GGCTTAACAGAATTAGCTAAGAAGTTTGAAGAGCGTAACTGAATTTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTT
genomic: GGCTTAACAGAATTAGCTAAGAAGTT-GAAGAGCGTAACTGAATTT-GCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTT
EST: gi|211270560|gb|FL015568.1|FL015568
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211265691|gb|FL015545.1|FL015545
EST:     AGGCTTAACAGAATTAGCTAAGAAGTTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AGGCTTAACAGAATTAGCTAAGAAGTT-GAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
EST: gi|211270564|gb|FL015572.1|FL015572
EST:     AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCT                         GTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG
genomic: AAGGCTTAACAGAATTAGCTAAGAAGTTGAAGAGCGTAACTGAATTTGCTgtaagcattt ... ccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
              atttaat  putative branch site (score: 4)
                                   tttttttgctccattt  putative PPT
                            tctataattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttctaggctatctgacatgcaatagaataaattccatggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC