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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagattatttgtagtcaagctaagctaaattgtggagaccatgtggatgtgcagaatggcgtgtattcataagttgtcaatatttgaaacctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG

Basic information

species Zea mays
transcript GRMZM2G017089_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 16
-------------------------------------------------------------------tgaagattatttgtagtcaag------ctaagcta-aattgtggagaccatgtggatgtgcagaatggcgtgtat-tcataa-gttgtcaatatttgaaacctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG
                                                                   | ||  |  || ||| |   |      ||| |||| | |||  |    ||   |  |    | |||    || |  |||||   ||   | || |   | | ||||||||||||||||| || || ||||||||||| ||||||||||| ||||||||||||||||||||||||||||| || ||||
gtatgcattgttgaaaacatcgagtttttgcctccttcctatttattttattaaagaaaaagatggtttaatgtatttagtaatgctgtattttctatgctatacttgctggccgcaaccgattcaataaaattttttgcagatcatattattaaaagtagtaatatcttgtgcagGGGATAATGGGAGTCTCTGGTTTTGGGATTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG

upper sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA15G15960.2 (Glycine max), 3'ss of exon 14
---------------------------------------------------------------------------------------tgaagattatttgtagtcaagctaagctaa-------attgtggagacc---atgtggatgtgcagaatggcgtgtattcataagttgtcaatatttgaaacctg--tgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG
                                                                                       |    |||| |  |   ||| ||    | |       ||  || |||     || ||||| |      |  | || ||| | |  || |     |||    ||||  |  ||| || ||||| ||| ||||||| ||||| ||||||||||||||||| || || |||   || || || || |||||||
gtatggaaacaaatttagactatcaggaaagcagtttgtggaataaattcaactaatccgtgccccaatttttcttaggcatgtgattaggaattaatgctccccaatcttgatttattgtgtcatactgaagaatttgatatggatattatttgtcccttgcattaa-actttatgcccttttttctcctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG

upper sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 3'ss of exon 15
------------tgaagattatttgtagtcaagctaa-gctaaattgtggagaccatgtggatgtg-cagaatggcgtgtattcataagttgt-caatatttgaaacctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG
            |   ||||  ||     |  |  |  | |    | ||      |  ||| || | || |||    |  |     || |  | | |||| ||       || ||| |||||||||||  | ||||| |||||||||||||||||||| |  || |||||     | ||||| || |||||||
gtatataatcatttctgattcctttcgtccctgtgattgttttcctttgatagtaaaatgggtgagacataatcattttcaactgaaactgattctatatatgtg-tgaatgaagGTGATAATGGAAGTATATGGTTCTGGGACTGGAAGAGTGGTCACAGTTTCCAACAGTCAGAAACTATCGTACAGCCTG

upper sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 14
lower sequence: PP1S169_73V6.1 (Physcomitrella patens), 3'ss of exon 13
--------------------tgaagattatttgtagtcaagctaag-ctaaattgtggagaccatgtggatgtg---cagaatggcgtgtattcataagttgtc-aatatttgaaacc--tgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG
                    |  |||||  || |  |||| | ||   || |||    | |  ||    || |    | || |    |  |   | | |||  | ||| ||  ||||    ||||||| |||||||||||  |||||||||||||||  |||||||| || || ||||| ||||  ||||| || || |||||||
gtttgcacgacagttctatttttagatttctttttctcaatccaaaattacattcccaacataatcgccatctatttcggattatacttcaaatagaggtttcctaatgttgaaaactgacgtgcagGTGATAATGGAAGTATGTGGTTTTGGGACTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTG

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|60342895|gb|DN209868.1|DN209868
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|31909551|gb|CD650975.1|CD650975
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|33091976|gb|CF051970.1|CF051970
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGCGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|37376961|gb|CF625047.1|CF625047
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|78023548|gb|DV491935.1|DV491935
EST:     GCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: GCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|76013075|gb|DT940245.1|DT940245
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|4967045|gb|AI691809.1|AI691809
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|6538870|gb|AW225009.1|AW225009
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|31406178|gb|CD484910.1|CD484910
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|71416740|gb|DR803804.1|DR803804
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|6865096|gb|AW360446.1|AW360446
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|33091991|gb|CF051985.1|CF051985
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|33093989|gb|CF053983.1|CF053983
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|5055899|gb|AI734786.1|AI734786
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|37382890|gb|CF628417.1|CF628417
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|101383542|gb|EB813827.1|EB813827
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|32933315|gb|CF038127.1|CF038127
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatgtgcagaatggcgtgtattcataagttgtcaatatttgaaacctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG
                                   aatatttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaagattatttgtagtcaagctaagctaaattgtggagaccatgtggatgtgcagaatggcgtgtattcataagttgtcaatatttgaaacctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA