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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaatctctacaaaccttgtgatcaacctgcatcaggaaaagagtgctaactcaatttatcagagtgctaactttcccgttattttttcttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGCCCTGAGATTGTTCCAAATCGGAGGCGCATGTTCTAACTGTCATGGACAA

Basic information

species Zea mays
transcript GRMZM2G025387_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025387_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g43410.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------------------------------------------cacaatctctacaaacct----tgtgatcaacctgca-tcaggaaaagagtgctaactcaatttatcagagtgctaactttcccgttattttttcttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGCCCTGAGATTGTTCCAAATCGGAGGCGCATGTTCTAACTGTCATGGACAA-
                                                                                             |||||   |   ||||    |  |   ||  ||   |||   | ||  ||| |   | |||||| | |||||||| ||| || || ||| || | |    ||||||||||||||||| |||||||||||||| ||||||||||||||||||| ||||||||||| ||| || ||| |||||||||||||||| || |  |||| 
gtaagtatattccgtaacacatcttaaagcaagctctttgataacaaaatgtgcatgtcccaaccatcctacaaggagaatgccaaagatttccaatcctaaagtacctttcttaagtagaatttgagctcaaacacaggctgcgaggcccatttattacagtgctaatttttccattttttgttttca----cagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACT-TCCTTTACAAT

upper sequence: GRMZM2G025387_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G02300.1 (Glycine max), 3'ss of exon 8
cacaatctctacaaaccttgt-gatcaacct-gcatcaggaaaagagtgct---aactcaatttatcagagtgctaactttcccgttattttttcttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGCCCTGAGATTGTTCCAAATCGGAGGCGCATGTTCTAACTGTCATGGACAA-
    |||        | |||| | | | ||| |   || |       || |   |      ||||         ||   |     ||||   || || |||| |||||||||||||||| ||  | |||||||| ||||||||||||||   || ||| || ||   || | ||         | ||   || |  |     ||  
---catcctagttctcattgttggttatcctagtgccaagttgtagatgtttgtagtgttgtttaattatactttacaatattaattatcaatt-ttcttgc-agGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTC-ACATAACCCATAGACGTCGCAAATAACCCCTGCATT

upper sequence: GRMZM2G025387_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G37260.1 (Glycine max), 3'ss of exon 7
----cacaatctctacaaaccttgtgatcaacctgcatcaggaaaagagtgctaactcaatttatcagagtgctaactttcccgttattttttctta-----ttgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGCCCTGAGATTGTTC-CAAATCGGAGGCGCATGTTCTAACTGTCATGGACAA
    |  | |     ||    | || |||  |  |   || |       || |       ||||         || | ||  |  ||||  |||| |      |  ||||||||||||||||| ||  | |||||||| ||||||||||||||   || ||| || ||    | || | |  |    | |     |   |  |||     
tcatcctagttctctcattgttggttatc--ctagtgccaagttgtagatgtttgtagtgttta-------attatcctttgcaatattaattctcaaatttcttgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGACATAACGCACATAACCCAAAGACGTCGCAAATAAGCTATGCTTT-

upper sequence: GRMZM2G025387_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G02260.1 (Glycine max), 3'ss of exon 7
----------------------cacaatctctacaaaccttgtgatcaacctgcatcaggaaaagagtgctaactcaatttatcagagtgctaactttcccgttatttttt---cttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGCCCTGAGATTGTTCCAAATCGGAGGCGCATGT--TCTAACTG-TCATGGACAA
                      |    ||||       ||| |  |  |    |||    | | |  ||   | ||  | | |   | || ||  ||  || |   ||       || |||| |||||||||||||||| ||  | |||||||| ||||||||||||||   ||  || ||  | ||    ||  |  | ||||  |  || |  || ||||  |   
gtacgctgctttcttccatatccttgttctcgttggtgcttatcctagaatgacatttt-agatgtttgtatattctctctgtttaattgttattttaaccatccattcccaaatttgttgc-agGATGGAAGAATTAACTATGACGAGTTTGTAGCCATGATGAGGAAAGGCAATCCAGATTTAGTAAACAACAGACGTCGCAAATAATCAAGTTGATCATAAA---

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|166438601|gb|EG254113.1|EG254113
EST:     AAAACTTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: AAAAC-TATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|24769066|gb|CA404195.1|CA404195
EST:     GAGATGCCAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTCCCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|60339637|gb|DN206610.1|DN206610
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|9952859|gb|BE639442.1|BE639442
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTCCCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|76909354|gb|DV163344.1|DV163344
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|60359360|gb|DN226333.1|DN226333
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|31359909|gb|CD444266.1|CD444266
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTA
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTA
EST: gi|33097720|gb|CF057680.1|CF057680
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|32831313|gb|CD970991.1|CD970991
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGC
EST: gi|5819190|gb|AI987396.1|AI987396
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|71760036|gb|DR957973.1|DR957973
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|71323405|gb|DR798352.1|DR798352
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|211267931|gb|FL119097.1|FL119097
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|148955625|gb|EC901287.2|EC901287
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTTCCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|149112525|gb|EE295388.2|EE295388
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|60401386|gb|DN234193.1|DN234193
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|211267932|gb|FL119098.1|FL119098
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|60343984|gb|DN210957.1|DN210957
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|60338425|gb|DN205398.1|DN205398
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|32833870|gb|CD973548.1|CD973548
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
EST: gi|5791292|gb|AI978084.1|AI978084
EST:     GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATNCAGATCAT                         GATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC
genomic: GAGATGACAAAACTATAAAAGAAATCATTGCTGAAGTAGATACAGATCATgtgagtatat ... ttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctaactcaatttatcagagtgctaactttcccgttattttttcttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGCCCTGAGATTGTTCCAAATCGGAGGCGCATGTTCTAACTGTCATGGACAA
                     tgctaac  putative branch site (score: 1)
                           ctttcccgttattttt  CT-rich tract
                                   ttattttttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacaatctctacaaaccttgtgatcaacctgcatcaggaaaagagtgctaactcaatttatcagagtgctaactttcccgttattttttcttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGCCCTGAGATTGTTCCAAATCGGAGGCGCATGTTCTAACTGTCATGGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA