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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG

Basic information

species Glycine max
transcript GLYMA07G05390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 3
--tattc-atgcaa-aactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
  | |||  |  ||  | | |     | || |  ||      || |  ||  || |||  |  ||    || | ||||  | |    |   |  |      |||||||| |||||||| ||||||||||| || ||||| || |||||||| || |||||| | ||||||
attgttctgtttaacgattctagaagctttatctacagtcggttcctgacagtgcatgcaacctaca--tggttaatggcttccatttatatcaca--ccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG

upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 2
tattcatgcaaa-actgtcactccattcttgaccagaaat--ttcctactatgtatgttatttatgcttgttcaa---tgcttacttgctcagttgc-tatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
       | ||   |  || |  ||| |    ||| ||    ||| | |  || || |||      ||||   ||   ||| |   | ||  |||     |    |||||||||||||| | |||||||||||||| || ||||| || ||||| || || || || || | |
-------gtaagcgccctcgccacatgccacgccacaagggattcttcccttggat-ttacactcacttgactaacgatgcgtttcttcttggttttgcgtggatagGTTGTGGAGATCTCCAAGGGAAGCAAGGTGAAGTACGAGCTCGACAAGAAAACGGGGTTCATCATG

upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 3
-tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
 | || | | ||||      |    || ||    |   |     |   |   ||  || |||        |||||    | |  |    |  | | | |||||||| |||||||| ||||||||||| ||||||||||| |||||||| || |||||| | ||||||
ttgttgaggaaaaataagtgcatggtttttttttaattacgatatttaacaaat-ctagttagctccaaacaatgaccgcgttatataattttttattcagGTTGTTGAGATCACAAAGGGAAGCAAAGTCAAATACGAGCTTGACAAGAAAACTGGACTGATTAAG

upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 3
-tattcatgcaaaactgtcac-tccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
 | | | ||   | |    |  | |||| || | || ||  ||  ||  |  | |  || ||    |  | || ||  | | |  |      || | |||||||||| |||||||| ||||||||||| || ||||| || |||||||| || |||||| | ||||||
atttgcttgtcgagcaaaaaagtgcattttttatcataatgtt--taacaaatctactagttcgcttcatacagtgactgcattatttacatctttatgcagGTTGTTGAGATCACAAAGGGAAGCAAAGTTAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG

upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G026470_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------tattcatgcaaaactgt---cactc--cattcttgaccagaaa---tttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG----------------------------------
                                                        |  ||  ||||  |||   |  ||  |||   |||  |   |   | ||  || ||   |    |    |   || |     |||| | |   ||  | |   |||||| ||||||||||| ||||| |||||||| || ||||| || ||||| ||||| ||  | || |||                                  
gtaagtatctgacgaatcccattccccagacccctcaccccagcaagcaagcaagcaagcagccaaagttgttctcgatcgacatgtgtgaatatggagcgtgtctgacgatccttccggtgcgcgtccgtccgtccgttacgtacgtggtgccgacgagcagGTCGTGGAGATCACCAAGGGGAGCAAGGTGAAGTACGAGCTGGACAAGAAGACGGGGCTCATCAAGGTGGACCGGATCCTCTACTCGTCCGTCGTCTACC

upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
           || | |    | | ||||      |||   |  | ||||| |||||||   | || |  |||  ||   |  |  | ||  |||   ||||||| ||||||||||| |||||||||||||||||||| |||||||||||||| ||| | || |||
---------gtaagttttttcctactctttgttctaaa---cagagtatgt-tgttatta--gattctctaatcattttatctttggatg--attattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG

upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatg-tatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
            | |||| ||  | |  | |||  |     ||| || |  | | |   |    |||| ||  || | ||  |   ||   || |   ||||| || |||||||| ||||||||||| || ||||| ||||| ||||||||||| ||  | || |||
----------gtattgtctcttaacttataacccaagtaagccttctttaatctctctctctctcttggtc--tgttaacgagag-agcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG

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|254344222|gb|GR851025.1|GR851025
EST:     GACCTGGAGCGCCTATGATTTTCAATTGT                         GTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
genomic: GACCTGGAGCGCCTATGATTTTCAATTGTgtaagttctg ... ctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
EST: gi|17400209|gb|BM176991.1|BM176991
EST:     GACCTGGAGCGCCTATGATTTTCAATTGT                         GTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
genomic: GACCTGGAGCGCCTATGATTTTCAATTGTgtaagttctg ... ctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
EST: gi|254315134|gb|GR830127.1|GR830127
EST:     GACCTGGAGCGCCTATGATTTTCAATTGT                         GTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
genomic: GACCTGGAGCGCCTATGATTTTCAATTGTgtaagttctg ... ctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
EST: gi|254344223|gb|GR851026.1|GR851026
EST:     GACCTGGAGCGCCTATGATTTTCAATTGT                         GTTGT-GAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
genomic: GACCTGGAGCGCCTATGATTTTCAATTGTgtaagttctg ... ctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
EST: gi|48574801|gb|CO036084.1|CO036084
EST:     GACCTGGAGCGCCTATGATTTTCAATTGT                         GTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
genomic: GACCTGGAGCGCCTATGATTTTCAATTGTgtaagttctg ... ctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
EST: gi|209698574|gb|BW652427.1|BW652427
EST:     GACCTGGAGCGCCTATGATTTTCAATTGT                         GTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
genomic: GACCTGGAGCGCCTATGATTTTCAATTGTgtaagttctg ... ctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
EST: gi|151399288|gb|EV269159.1|EV269159
EST:     GACCTGGAGCGCCTATGATTTTCAATTGT                         GTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
genomic: GACCTGGAGCGCCTATGATTTTCAATTGTgtaagttctg ... ctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
                           tgcttac  putative branch site (score: 2)
     tatgttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG