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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA

Basic information

species Zea mays
transcript GRMZM2G028037_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataac---atcttgaaccttcacatacccatctaataacatttttt-----ttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
         || | |||||||| ||     |||||  |||    |||||   ||  ||||   ||   ||   |||| |||    | ||      |||||| ||| || ||| || ||||| ||||||||||| ||||||| ||| || ||||||||||| || ||||| |||||||||||||||||||||||||| ||||| |||||
-------gttgcgttaaatttggccca-actgtttcatttcagtataactctattctgaagtgtcttgtatttatctgatatttgtcttggataattgtattaaacagGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
---aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaa-atagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
   |  |||    |  | | |  | |  | | ||| | | | || | ||      ||| |  ||  | |       | ||    |  | |    || ||  |||  ||  ||||||| |||||| ||||||||||||||||||| || || ||||| || || || |||||||||||||||||||||||| |||||||||| ||
tctatcattggtagaacaagaactcaaaactattgctgtatatttttatg----tttggattttgtccttttttatttatgttctcatgtggaaattaatgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
-aggatt--ttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
  ||||   |||||   |  |  |    | |  || ||    |  |  |      |  | || |   ||   | ||   ||| |  || | ||| |    ||| |||  ||||||| |||||| ||||||| ||||||||||| ||||| ||||| || || || |||||||||||||| ||||||||| |||||||||| ||
gtggatggattatggattggaacttcaaacttctgcttatactctttgttttgattatatccattgtatgttc-tcatgtaaaagattatatgtttt--gtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 3
-aggattttatgtg---ctaaatttgaccagtgttgttttgt--tttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaa-atagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
    || ||  ||    ||  |  | |  | | ||| | | |  ||| |  |   || |||  ||||   ||       | ||    |  | |    || ||  |||  ||  | ||||| |||||| ||||||||||||||||||| || || ||||| || || || |||||||||||||||||||||||| |||||||||| ||
ctctatcttgggtagaactggaactcaaaactattgctgtatattttatgtttgtattttgtccctttttat-------ttatgttctcatgtggaaattaatgtagGATCCATTCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 2
aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaacct--tcacatacccatct---aataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
   | |  || || |   | ||    |   | |  |    |   | || ||| ||  | |  | |  |     |||   || |||| ||||||| | |  |  || | |  ||||||| || ||| | || |||||||||||||| |||||||| || ||||| || |||||||| |||||||| ||| | || ||  |||| ||
-ataatgcatttgttctttctgcttggcactatgctac--taataaaaaatcatggtcatgattaattctttttctggtaacaacaatttttttatgttga--agGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
-----aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacat-cttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
     |  ||    ||| ||   | ||   ||   | || | |||     |   || | | |       |||     |||  |||||    |    | |  |  || ||| |||||||| || ||| | || |||||||||||||| ||||||||||| ||||| || |||||||| |||||||||||| ||||||| ||||    
ttcctataatgcattgttctt--tctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 3
----aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacat-cttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
    |  ||    ||| ||   | ||   ||   | || | |||     |   || | | |       |||     |||  |||||    |    | |  |  || ||| |||||||| || ||| | ||||||||||||||||| ||||||||||| ||||| ||  ||||||| |||||||||||| | || || |||||   
tcctataatgcattgttctt--tctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT---

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
-aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
    |    |||   |  |  |    | |  || ||    |  |  |      |  | || |   ||   | ||   ||  |  || | | | |    ||| |||  | ||||| |||||| ||||||| ||||||||||| || || ||||| || || || ||||||||||| || ||||||||| |||||||||| ||
tgaaagagaatggattggaacttcaaacttctgcttatactctttgttgtgattatatccattgtatgttc-tcatgtacaaaattatatatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 2
aggattttatgtgctaaatttgaccagtgt-tgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaa---tagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
       ||||| |||      |||  ||    | || || | ||  |     ||||    || | |     |   ||    || |||||  ||        || | | || ||||| || ||| |  || ||||||||||||| |||||||| || ||||| ||||| |||||||| ||||||||||| |  ||||| || ||
------gtatgt-ctatcgcaaacctctgcacatcttcttctttctgagggctttgaggtgtctcgtctaattaccatgtttttcttttttcatttgggttcagGGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
aggattttatgtgctaaatttgaccagtgttgttt------tgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
     ||||   |  | | |    |  || | |||      || ||||| |   ||   | ||   | | ||     ||| || | |    |||| |||    ||| | |  ||||||| ||||||||||| || ||||||||||| || |||||||| || || || || ||||||||||| ||||| ||||| ||||| || ||
-atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattatta-atgttt-tctcatgataacaattttatat---gtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataac-attttttttgtat-caaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
      | ||    | |||||||  | |||  ||      | |||| |    | |     |   ||    ||||  ||   | |  | || | | |    || | |  ||||||| || ||| |||| |||||||||||||| ||||||||||| || || || || ||||||||||| ||||||||||| |||||||| ||
-ttgactgatagcatcaatttgagaattgtgattagaaaatttcattatggttggtggtatttaatgtt-atctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA

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|32938653|gb|CF043472.1|CF043472
EST:     CGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAA                         AGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
genomic: TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAAgcaagtatct ... tatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
EST: gi|6021366|gb|AW066294.1|AW066294
EST:     TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAA                         AGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
genomic: TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAAgcaagtatct ... tatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
EST: gi|32938832|gb|CF043651.1|CF043651
EST:     CGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAA                         AGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
genomic: TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAAgcaagtatct ... tatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
EST: gi|71595774|gb|DR906525.1|DR906525
EST:     CGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAA                         AGTCATTGCCTCTACCATGGGCCATTACAATGAAAATTGCTCTTGGTGCTG
genomic: TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAAgcaagtatct ... tatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
EST: gi|7238071|gb|AW573443.1|AW573443
EST:     TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAA                         AGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
genomic: TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAAgcaagtatct ... tatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
EST: gi|50323063|gb|CO518189.1|CO518189
EST:     TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAA                         AGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
genomic: TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAAgcaagtatct ... tatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
EST: gi|211053378|gb|FL364311.1|FL364311
EST:     TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAA                         AGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
genomic: TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAAgcaagtatct ... tatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG
EST: gi|19436855|gb|BM953265.1|BM953265
EST:     TGGGTATGAATTTATGCCCCGGGGAAGTTTGGAGAATCATCTTTTTAGAA                         AGGCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGGGCTG
genomic: TGTGTATGAATTTATGCCCCGTGGAAGTTTGGAGAATCATCTTTTTAGAAgcaagtatct ... tatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacatcttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
                            taataac  putative branch site (score: 1)
                                    ttttttttgt  CT-rich tract
                         atctaataacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - -tgtgcta
- - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatac