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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttttgaattataatgtcataatctttgtatttttttaattaaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

Basic information

species Glycine max
transcript GLYMA13G21480.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os09g39320.1 (Oryza sativa), 3'ss of exon 11
gtat-gtatt-taaaaaataaactatactgtttcttcttttttagtattttt---tgaattataatgtcataatctttgtatttttttaattaaccatgtgttattttatcatttg-cagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
|||| ||||| |   | ||   || |  |||  ||| | | |   |  |||    |||| | | |  ||  ||     | |||  |   | ||   | ||  | | |  |   ||| ||||||||||| ||||| ||||| ||||||||||  || || ||||||||| | ||| |||| |||||||| ||||| ||||||||||| ||||| ||||| 
gtattgtattatctcatattctcttttttgtgacttttgtctacctgctttcacatgaacttttaactcccaaaacaagaattcat---actatttaagtaatctctggttgcttgacagGCAAAGGGAATGAACTATCTACATAAACGTAGCCCTCCTATTGTTCATCGTGATTTGAAGTCTCCAAATCTTCTAGTTGACAAGAAGTATACCGTGAAA

upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G059671_T03 (Zea mays), 3'ss of exon 9
gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttttgaattataatgtcataatctttgtatttttttaattaaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG-
              |      ||||||          |   | |    ||| | ||  |||     |    | ||  |||  || |  |   | ||  || || | || | |||||||| |||||||| ||||||||||| |||||||| || || || ||  | ||||| || || ||||||||  | |||||||| || || || |||||  
----------tggcaccgctatatacttcaataaagctgacattggcctttcagttgaaat--tgaagcaatcgtcgtttaatactctattgtttgc-atcttct-atgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAG

upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttttgaattataatgtcataatctttgtatttttttaattaaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
              |      ||||||          |   | |    ||| | ||  |||     |    | ||  |||  || |  |   | ||  || || | || | |||||||| |||||||| ||||||||||| |||||||| || || || ||  | ||||| || || ||||||||  | |||||||| || || || ||||| 
----------tggcaccgctatatacttcaataaagctgacattggcctttcagttgaaat--tgaagcaatcgtcgtttaatactctattgtttgc-atcttct-atgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA

upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttt-tgaattataatgtcataatctttgtatttttttaatt--aaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
                       || |||||  |   || |  ||  | | ||  | || |  || | ||||| || ||| || |  |  |||  | | |    || ||  |  ||||| ||||| |||||||||||||| || || ||||| || ||||| ||||||||||| |||||||||||| |  | |||||||| ||||||||||| |||
----------------------gta-tgtttaattccttatgttacatgtatgggtgattacttcctgatcttggtgtttcttcacatggaactttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG

upper sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 10
gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttttgaattataatgtcataatctttgtatttttttaattaaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
 ||| | ||||   | |    |||   | | |  |||||      |    | | || |  | | || || |  ||  ||||||           | || |||||  |    ||||| ||||| |||||||||||||||||||| ||||| |||||||||||| ||||| |||| |||||||||||| | |||||||| ||||| || ||||||
-tatttttttagtgatt--gttatttggatgcaccttttaccagctaaaataacttgttttattatcatttccgtgctttttt-----------tttttttttaaaacaaacagGCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAG

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|9820117|gb|BE555627.1|BE555627
EST:     CCAAAGAAGTATTGGATGAGAGGCGTAGGCTTGGTATGGCTTATGACGTG                         GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA
genomic: CCAAAGAAGTATTGGATGAGAGGCGTAGGCTTGGTATGGCTTATGACGTGgtatgtattt ... tcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA
EST: gi|21888649|gb|BQ741862.1|BQ741862
EST:     GCGTAGGCTTGGTATGGCTTATGACGTG                         GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA
genomic: GCGTAGGCTTGGTATGGCTTATGACGTGgtatgtattt ... tcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA
EST: gi|51335181|gb|CO979047.1|CO979047
EST:     TATGGCTTATGACGTG                         GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA
genomic: TATGGCTTATGACGTGgtatgtattt ... tcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA
EST: gi|19271170|gb|BM887426.1|BM887426
EST:     CCAAAGAAGTATTGGATGAGAGGCGTAGGCTTGGTATGGCTTATGACGTG                         GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA
genomic: CCAAAGAAGTATTGGATGAGAGGCGTAGGCTTGGTATGGCTTATGACGTGgtatgtattt ... tcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA
EST: gi|51344716|gb|CO985449.1|CO985449
EST:     CCAAAGAAGTATTGGATGAGAGGCGTAGGCTTGGTATGGCTTATGACGTG                         GCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA
genomic: CCAAAGAAGTATTGGATGAGAGGCGTAGGCTTGGTATGGCTTATGACGTGgtatgtattt ... tcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcataatctttgtatttttttaattaaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
                        aattaac  putative branch site (score: 2)
                                        ttttatc  putative PPT
               tatttttttaattaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttttgaattataatgtcataatctttgtatttttttaattaaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA