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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgcatgcgtcaatctatgcaagattttgctggcaacttgtgcagtttttgcatttttataatttttccttattctatgttccttgttccatactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA

Basic information

species Zea mays
transcript GRMZM2G116087_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116087_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g55870.1 (Oryza sativa), 3'ss of exon 4
tttgcatgcgtcaat-ctatgcaagattttgctggcaacttgtgcagtttttgcatttttata----------atttttccttattctatgttccttgttccatactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA
          | | | |||| |     ||  ||||  ||| ||||| ||   |||||||||||          ||  |  | | ||||   || | ||||| ||  ||||||| ||||||||||| || |||||||| ||||||||||||||||| |||||||||||||| ||||||||||||| ||| || |||||||| || 
----------ttagtactatactgttgttcactggtgactcgtgcaattag-gcatttttatattgggaaattatgctcacctgttcttgttttcctgttctatcatccagGCGCTCTCCAAAAGAATTCACTATGGTAAGTTTGTGGCAGAGGCTAAGTTTCAAGAGTCTCCTGAAGCTTACATGCCTGCGATAATAGCACAG

upper sequence: GRMZM2G116087_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G06660.1 (Glycine max), 3'ss of exon 3
tttgcatgcgtcaatctatgcaagattttgctggca-acttgtgcagtttttgcatttttataatttttccttatt-ctatgttccttgttccatactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA
||  ||| | | | ||| ||  ||  |||| |  || | |  || |    | |     |   ||||     || |  ||||  | |||   |   | | ||||| ||||| ||||| ||||||||||| || ||||| || ||||| |||||||||||  |||||   |  ||     | |||||   |||  ||
ttcccattcttgactctctg--agcatttgatatcataatcatgtaacggtagttcagtacaaattccgagttttcgctataatgcttcggcaccattacagGCTCTCTCAAAAAGAATCCACTATGGCAAATTTGTTGCTGAGGCAAAGTTTCAAGATGCCCCTTCTGAATATGTAGCTGCCATTGAAGCGAAA
















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|149033875|gb|EE155016.2|EE155016
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|148966792|gb|EE017885.2|EE017885
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCCG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|149029771|gb|EE286265.2|EE286265
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|60356414|gb|DN223387.1|DN223387
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|148973538|gb|EE024639.2|EE024639
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|78125597|gb|DV543981.1|DV543981
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|148938252|gb|EC882544.2|EC882544
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAA
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAA
EST: gi|149088482|gb|EE177591.2|EE177591
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|78089260|gb|DV517634.1|DV517634
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|211039898|gb|FK958023.1|FK958023
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|71762890|gb|DR960827.1|DR960827
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|94479717|gb|EB708675.1|EB708675
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|31352097|gb|CD436454.1|CD436454
EST:     GATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|211304785|gb|FL143334.1|FL143334
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|78111571|gb|DV529968.1|DV529968
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|148952137|gb|EC897931.2|EC897931
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|71448582|gb|DR829632.1|DR829632
EST:     GTGATGGTAATGCTGGATTCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|149086680|gb|EE176220.2|EE176220
EST:     GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAG                         GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
genomic: GTGATGGTAATGCTGGATCCAATGCTCTTTGTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTT
EST: gi|148961522|gb|EE012274.2|EE012274
EST:     TGATGGTAATGCTGGATCCAATGCTCTTTTGTGACACAACCTGCTTGCAG                         GCACCTCCTCCAAAAGGATCCACTATGGGAAGTTT
genomic: TGATGGTAATGCTGGATCCAATGCTCTTT-GTGACACAACCTGCTTGCAGgtacagctga ... catactccagGCAC-TC-TCCAAAAGGATCCACTATGGGAAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgcatttttataatttttccttattctatgttccttgttccatactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA
                  tttttccttattctat  CT-rich tract
        atttttataatttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgcatgcgtcaatctatgcaagattttgctggcaacttgtgcagtttttgcatttttataatttttccttattctatgttccttgttccatactccagGCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC