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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactggaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT

Basic information

species Glycine max
transcript GLYMA05G36600.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 3
gtaactggaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgccaatttctcacattt-tcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
                    | | |||||       || ||    |||  ||   |    |  | |  | || |     | ||| ||||| | |   ||||||  | | |||| ||||||||||| || ||||||||||| ||||||||||| |||||||||||||| || ||||||||||| || || ||||| || ||||||||||| ||
-----------------gttagtaatgacaagacattcatgtg--cttagttaactcaagc--ggtgattctgtggaagccattgctcacttctgctctttcatgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTGCTGGCCTGAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT

upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 3
gtaactggaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
                   |     |||   |||   |  |  | ||  | |  ||  |   |     ||   |      | || || |  ||||  |||      | |||| |||||||||||||| ||||||||||| ||||||||||||||||||||||| || |||||||||||||| || || ||||| || ||||||||||| ||
----------------gttagtaactgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggc-ttacttccttatgttttgttttt-----tgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT

upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 3
gtaactggaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
                   |     |||   |||   |  |  | ||  | |  ||  |   |      |         || || ||    || |  |||    | | |||| |||||||||||||| ||||||||||| ||||||||||||||||||||||| || |||||||||||||| || || ||||| || ||||||||||| ||
----------------gttagtaactgaacaattctgctggttacctctagtagttgttatgtaaaaacgtggcggc-tcacttccttgtgttgtgtttt----tttgcagCGTACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT

upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaactggaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgccaatttctcacattttcctttcaactgtac--agCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
                      |  |   || ||     ||   |   ||  || |  ||  |   | |  ||        |||  | |  |  |  |||  ||| | |  ||||||||||||||||||||| ||||| || || |||||||||||||| |||||||| ||||||||||||||||| ||||||||||||||||||||||| ||
--------------------gttagtttgttgttatatatgtggtggagag-gtatctttattatctgtatttggtgattgattgtttatttggtgtttttgactttgcgtagCTTACTTCAATGATGCTCAAAGGCAAGCTACTAAGGATGCTGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATTAATGAACCTACTGCTGCTGCTAT

upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaactggaagtctggaac-aactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatg-ccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
      |  ||| ||     || ||  |  || | |    |      | ||  | |   || ||   | ||  ||  ||    |||  | |  |  |  ||     ||  |||||||||||||||||||||| ||||| || ||||||||||| ||||| |||||||| ||||||||||||||||| || || ||||||||||||||||| ||
------gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttct-tatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT

upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 3
---------------------gtaac-tg-gaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
                      |||| || || || | ||||  | |       | |  || || ||| |  |||    | ||  |  ||  | | || | |  || |       ||||| | ||||    ||||||||||||||||||| ||||||||||| || ||||||||||| || |||||||| || ||||||||  ||||||||||||| || |||||||| || ||
gtgagtatcactcttctagatataacgtgtgaggttttgaactgcccgct-tacactcttcttgaaatgtgaattagcattttgttcattaggatgttttactcatatta---gctttccatgcaacc-cgcagCTTACTTCAATGATGCCCAGAGGCAGGCTACAAAGGATGCTGGCGTTATTGCTGGCCTGAATGTTGCACGAATTATTAATGAGCCAACTGCTGCAGCTAT

upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
gtaactggaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
       | | | |  ||||  |  ||| ||  |         |  |||  ||||||  |  ||   |  ||| | |  | ||| || |||  |||          ||||||||||||||||||||| ||||||||||||||||||||||| ||  | |||||||| || |||||||| ||||| || ||||||||||| || || |||||
-------gtaatgtaaaacagtt--tgatttgatggatgaagtaaattg-ctgtttttctgttgagatgacttatgtttctatt-cttacaacttc----------tacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT

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|193429512|gb|FK394460.1|FK394460
EST:     GGAAGCATTCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGT
genomic: GGAAGCATTCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaa ... aactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGT
EST: gi|16276964|gb|BI942132.1|BI942132
EST:     GGAAGCATGCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCGAAG-ATGCTGGTGTCATT
genomic: GGAAGCATTCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaa ... aactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACC-AAGGATGCTGGTGTCATT
EST: gi|151402800|gb|EV272613.1|EV272613
EST:     GGAAGCATTCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAG                         CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG
genomic: GGAAGCATTCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaa ... aactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcctgcttttgcttttatgccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
                           ttctcac  putative branch site (score: 2)
                                   ttttcctttcaact  CT-rich tract
               ttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactggaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC