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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagtcaggcagttaccgttttgcctattttcatctgttccttctgtttgtttcttcccaccaaattttgcatcattgtatgtttatttattttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTGGCTGCTAACTCATGCAGCTGTGAGTTG

Basic information

species Zea mays
transcript GRMZM2G094959_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094959_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g47780.1 (Oryza sativa), 3'ss of exon 5
--ttgagtcaggcagttaccgttttgcctattttcatctgttccttctgtttgtttcttcccaccaaattttgcatcattgtatgtttatttattttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTGGCTGCTAACTCATGCAGCTGTGAGTTG
  |   ||  |      |  |  | |  || | |     |  |||| | |||||  | | |   |    |     |  |   |  ||   ||    |||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||||| ||
tttcttgttggatga--aatggatggaataatatagaagggcccttttttttgtcacattcattctgcatcattttggtccgacattctcttgacctttcagAAAGAGCTAATATCTGGTGATCAGAACGGAAACATACGTGTGTGGGATTTGGCTGCTAACTCGTGCAGCTGTGAGCTG

upper sequence: GRMZM2G094959_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G09170.1 (Glycine max), 3'ss of exon 5
ttgagtcaggcagttaccgttttgccta---ttttcatctgttccttctgtttgtttcttcccaccaaattttgcatcattgtatgtttatttattttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTGGCTGCTAACTCATGCAGCTGTGAGTTG
    ||     | ||   |   |  | |   |  |||  |     ||||  | ||||||| |       || | |||   | | | ||    |  |  | ||||  || |||||||||||||| || ||||| ||||| ||||| ||||||||| | || || |||||||| || || |||
--tggttccttaatttttgcaatatccagaatactcagattgcagttcttatagtttcttgctttgtggttct-cattgattttttttctggtgatcctacagACTGAACTAATATCTGGTGACCAAAATGGCAACATTCGTGTGTGGGATTTGACAGCAAATTCATGCAGTTGCGAATTG

upper sequence: GRMZM2G094959_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G29940.1 (Glycine max), 3'ss of exon 5
ttgagtcaggcagttaccgttttgcctattttcatctgttcc---ttctgtttgtttcttcccaccaaattttgcatcattgtatgtttatttatt---ttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTGGCTGCTAACTCATGCAGCTGTGAGTTG
     |     | ||   | | |  | |   | ||| | |     ||||  | | || || |       |||| |||   | | | ||| | |  |     | ||||  || |||||||||||||| || ||||| ||||| ||||| ||||||||| | || || |||||||| || || |||
-----ttccttaatttttgctatatccagaataatcagattgcagttctcataggtttttgctttgtggtttt-cattgatttttatttttctggtgatcctacagACTGAACTAATATCTGGTGACCAAAATGGCAACATTCGTGTGTGGGATTTGACAGCAAATTCATGCAGTTGCGAATTG

upper sequence: GRMZM2G094959_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0007g08080.t01 (Vitis vinifera), 3'ss of exon 6
ttgagtc--aggcagttaccgttttgcctattttcatctgttccttctgtttgtttcttcccaccaaattt-tgcatcattgtatgtttatttattttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTGGCTGCTAACTCATGCAGCTGTGAGTTG
| || ||  | |   |       | || |  |||    |   || | |||  | ||      |  |  | | |   |||    || ||| | |  |||  ||||  || || ||||||||||| || ||||| || |||||||| ||||||||| | || || ||||||||||| || |||
tggaatcttatgatataggaacatggcttggttttggattggccat-tgtaagattacaaatataatgtgtatttgtcacc--atatttttctggtttcacagACTGAACTGATATCTGGTGACCAAAATGGCAATATACGTGTGTGGGATTTGACAGCCAATTCATGCAGCTGCGAATTG

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|71304854|gb|DR788542.1|DR788542
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAATATCTGGTGATCAGAATGGAA-CATACGTGTATGGGATTTG
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
EST: gi|91872736|gb|EB402693.1|EB402693
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
EST: gi|148964671|gb|EC905953.2|EC905953
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAAAATCTGGTGATCAGAATGGAAACATACGT
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGT
EST: gi|31355657|gb|CD440014.1|CD440014
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
EST: gi|74244011|gb|DT651925.1|DT651925
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
EST: gi|71444669|gb|DR825719.1|DR825719
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
EST: gi|149021614|gb|EE045799.2|EE045799
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
EST: gi|71427439|gb|DR808489.1|DR808489
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGAATTG
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
EST: gi|32941525|gb|CF046344.1|CF046344
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
EST: gi|148985739|gb|EE029756.2|EE029756
EST:     AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAG                         AAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG
genomic: AATATGAAAGTCGTGCTGCAGTTAACACTGTAGTTCTGCACCCAAATCAGgttagaatca ... attttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgtttcttcccaccaaattttgcatcattgtatgtttatttattttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTGGCTGCTAACTCATGCAGCTGTGAGTTG
                                      tttatttattttttc  CT-rich tract
                  aaattttgcatcattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagtcaggcagttaccgttttgcctattttcatctgttccttctgtttgtttcttcccaccaaattttgcatcattgtatgtttatttattttttcagAAAGAGCTAATATCTGGTGATCAGAATGGAAACATACGTGTATGGGATTTGGCTGCTAACTCATGCAGCTGTGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - caggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtatg