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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG

Basic information

species Zea mays
transcript GRMZM2G171745_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g30840.2 (Oryza sativa), 3'ss of exon 7
ttattattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
    | ||| | || | || |  ||      ||  ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||
----ttttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagcagGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG

upper sequence: GRMZM2G171745_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g30840.1 (Oryza sativa), 3'ss of exon 7
ttattattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
 |  | ||| | || | || |  ||      ||  ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||
-tgattttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG

upper sequence: GRMZM2G171745_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 7
-------------ttattattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
              |  | ||| | || | || |  ||      ||  ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| |||||||      
catgtgttccattctgattttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagTTGAACAATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACC------

upper sequence: GRMZM2G171745_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g30840.3 (Oryza sativa), 3'ss of exon 7
----------------ttattattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
                 |  | ||| | || | || |  ||      ||  ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||         
tgtcatgtgttccattctgattttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagAAGTTGAACAATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCG---------

upper sequence: GRMZM2G171745_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G25690.2 (Glycine max), 3'ss of exon 7
------ttattattattt--ttcagtgttcatataatggcagctactgtatt---------aaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
       ||  | ||| |   | | | | || | |  |    || ||||  |          ||||   | | |||    | || |||||||  |||||||||||| ||| | ||||||||| ||||| |||||  | |||||||| ||| |   |||||||||||| ||| | ||||||| |||||| || ||   |||         
gataatataaaagtatctgactaattatacacacatagttgcctgctgttctttatgcttggaatatattggtcgacgtgtcttacttacttcgtggcagAAGTTACACACTGTAAGCAGGCCGACATCGACTTCAGAGGGCATGAGGAGATCTGCTCTGAATCTGGTGGAGTGATGGATTATGAAGAAGATCGAAGCCG---------

upper sequence: GRMZM2G171745_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G25690.1 (Glycine max), 3'ss of exon 7
ttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
   | |||||       |  |    |  ||     || ||  |  ||||   | | |||    | || |||||||  |||||||||||| ||| | ||||||||| ||||| |||||  | |||||||| ||| |   |||||||||||| ||| | ||||||| |||||| || ||   ||||||||| ||
--ctaattatacacacatagttgcctgctgttcttta-tgcttggaatatattggtcgacgtgtcttacttacttcgtggcagaagttacacactgtaagcagGCCGACATCGACTTCAGAGGGCATGAGGAGATCTGCTCTGAATCTGGTGGAGTGATGGATTATGAAGAAGATCGAAGCCGACCAAAGAG

upper sequence: GRMZM2G171745_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 7
ttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
   ||   || |       |  | | |   |    |    |  |      |||||    |   | || ||||| |  |||||||||||| ||| | ||||||||| ||||||||||| || ||||| || ||| |   ||||||| |||| ||| | ||||| |  || || || ||   |||||| || ||
---ttgaaatgtgcagacatataaaaatgagttattcaaatgctgggatatgttggtcgattgtcttacttacgttgtggcagaagttacacactgtaagcagGCCGACATTGACTTCCGAGGGCACGAGGAGATCTACTCTGAACCTGGTGGAGTGATGGACTACGAGGAAGATCGAAGCCGACCCAAGAG

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|74242378|gb|DT650292.1|DT650292
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATC-A-                         -AGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|60346665|gb|DN213638.1|DN213638
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATC-A-                         -AGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|78118434|gb|DV536820.1|DV536820
EST:     CCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAAATCA-G                         CAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGG
genomic: CCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAA-TCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGG
EST: gi|211195518|gb|FL100642.1|FL100642
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         --G-CAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|86472724|gb|DY239094.1|DY239094
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATC-A-                         -AGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|71427328|gb|DR808378.1|DR808378
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         --G-CAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|148943925|gb|EC889005.2|EC889005
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         --G-CAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|148972927|gb|EE023942.2|EE023942
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         --G-CAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGG
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGG-
EST: gi|78112152|gb|DV530548.1|DV530548
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         --G-CAGACATTGACTTACGGGGGCATGACGAGTTTCTCTTTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|74242379|gb|DT650293.1|DT650293
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         --G-CAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGN
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGG-
EST: gi|60340320|gb|DN207293.1|DN207293
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATC-A-                         -AGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|76931006|gb|DV172592.1|DV172592
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         --G-CAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|211192853|gb|FL432744.1|FL432744
EST:     ACCAGAAAGAATTTGAAGACAGAKTGGAAGAGGCCAAAAAATCAATCAAG                         CAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|78118433|gb|DV536819.1|DV536819
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         CAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|32809485|gb|CD961719.1|CD961719
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCC-AAAAATCAATC-A-                         -AGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|76931005|gb|DV172591.1|DV172591
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATC-A-                         -AGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTTTTTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|71427327|gb|DR808377.1|DR808377
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATC-A-                         -AGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTTTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|31352916|gb|CD437273.1|CD437273
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATC-A-                         -AGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA
EST: gi|89251568|gb|DY623354.1|DY623354
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         --G-CAGACATTGACTTACGGGGGCATGACGAGTTTCTCTTTGAATCTGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... acaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
                                      aagttaaacaatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - -ttcatat
- - - - - - - - - - - - - - - - -gctactg
- - - - - - - - - - - - - - - - - - - - - - - - - tgttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagaag