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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattactttatacataatccccaaaatacagtttacttgagcattaagcattgttatgactgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG

Basic information

species Zea mays
transcript GRMZM2G123140_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123140_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 11
aaattactttatacataatccccaaaatacagtttacttgagcattaagcattgttatgactgaaaacttttcattgcatcttctgatgaaaaccaa----cagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG
  || |  | | |  |  |  |   | |    |     ||   ||| |   | | |||     || |  |  | ||    |   |||| |||||  |    ||||||||||||||||| || ||||| ||||||||| ||||||||||||||||||||||||| || || |||||||| |||||||| ||||| ||||||||||
--ataa--tgagagttgcttactttacttttttccctctgctgattgaaactagatatataacaagagctgacctttttccaattgataaaaactgatgtccagGCTGCAAGCAACTCGTCACAGAATGTGGAGCTCCTGCTGCAGGAGAGCAGCACCCACCCTGATGGTGGGAGCCTGGTGGTGTTCGCGACGGTGGACGTGG

upper sequence: GRMZM2G123140_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA09G34070.1 (Glycine max), 3'ss of exon 10
aaattactttatacataatccc-caaaatacagtttacttgagcattaagc--attgttatg-actgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG---
|||||     ||   ||||        | |  || || ||       |||   |  ||| |  | |  |||| ||   ||     || | |   | |    ||||  || |||||||||||||||||||| ||||| |||||||| ||||   ||||| |||   |    || ||| | || ||||   | ||| | |||||||   
aaattgtgaaatttttaatttgatgtgaaatggtctaattagaatgcaagtgaaaggttctctattccaaaccttaggtta----ttgttacatatatatgcagGTAGCGAGCAACTCATCCCAGAACGTAGAGCTAATGCTGCAAGAGAATTGCACCGACC---AATCTGGAAGCATAGTAGTGTACACAACCATCGACGTGGATT

upper sequence: GRMZM2G123140_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA01G01850.1 (Glycine max), 3'ss of exon 10
--aaattactttatacataatccccaaaatacagtttacttgagcattaagcattg--ttatgactgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG---
   | ||  |||||      |      ||   |  ||| |  |     |   |  |  ||   | |  |||| ||   ||     |||  |   | |    ||||  ||||||||||||||||||||||| ||||| |||||||| |||||  ||||| |||   |    || ||||| || ||||   | ||| | |||||||   
tagagtttttttatttgatgtgaagtgaaatgatcttattaaaatgcaagtgaaaggttttctattctaaaccttaggtta----ttcctacatatatatgcagGTAGCAAGCAACTCATCCCAGAACGTAGAGCTAATGCTGCAAGAGAGTTGCACCGACC---AATCTGGAAGCCTAGTAGTGTACACAACCATCGACGTGGATG

upper sequence: GRMZM2G123140_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv02s0012g02030.t01 (Vitis vinifera), 3'ss of exon 10
------aaattactttatacataatccccaaaatacagtttacttgagcattaagcattgttatgactgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG---
      |||| | |    |   ||||  |   |    ||   | | |   || | |    |||  | ||   |  ||  |  |   ||| | ||| |  |    |||  || ||||| ||||| |||||||| |||||||||||||| |||||| ||||| |||   |   ||| |||| |||||| |   | ||| | |||||||   
gagatgaaataagtgctgaaccaatcttctttaggaggtgctcatcaattttcatctaatttaaaagtgtgtaaatt--agagacccttttcatgcatgc----agGTGGCCAGCAATTCATCACAGAACGTAGAGCTCATGCTGCAAGAGAGCTGCACCGACC---AGTCCGGCAGCCACGTGGTTTACACCACCATTGACGTGGATG

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|31910760|gb|CD651585.1|CD651585
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|71321764|gb|DR797569.1|DR797569
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|22819056|gb|BU499146.1|BU499146
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|5555586|gb|AI881537.1|AI881537
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|71329968|gb|DR801717.1|DR801717
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|87157207|gb|DY401996.1|DY401996
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|30306491|gb|CD001164.1|CD001164
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|26559801|gb|CA832036.1|CA832036
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|31558675|gb|CD527887.1|CD527887
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagcattgttatgactgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG
                                    ttctgat  putative branch site (score: 3)
                  aaaactttt  TA-rich tract