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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaccttcaccttcactattccatttgggctacattttcttctgtctatttggtgacttctgtttctaaatcatggtcctgttttttttccccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT

Basic information

species Glycine max
transcript GLYMA09G12430.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G12430.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g42380.1 (Oryza sativa), 3'ss of exon 3
aaccttcaccttcactattccatttgggctacattttcttctgtctatttggtgacttctgtttctaaa-----tcatggtcctgttt--------tttttccccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
          || |||| |||   |||   | || ||    || ||  ||   || |||   |  ||||     | | | | |||  |        |||    |  | | |||||||||| ||||||||||| ||||| |||||||| | ||| || ||| ||||||||||| |||| || || ||||| |||||||||||||  ||||||||
----------tttactagtcc---tggaagatatctttagatgcctggttctagagttcctctgttaaaactacttaggtttctgcatatcctcagtttgctacttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGGGTCGTATCATAGCTGGAACATGTCATAGTGCTAAGATGAACAGGACCAT

upper sequence: GLYMA09G12430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 3
------aaccttcaccttcactattccatttgggctacattttcttctgtctatttggtgacttctgtttctaaatcatggtcctgttttttttccccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
      | |  |       | ||||| | |||| |||  |   |||        ||  |||    || |       | || |||  |  || ||        ||||| || |||||||| ||||| |||||||||||||||| |||||| ||| |||| || ||| |||| || ||||| || ||||| |||||||  ||||||||
gttgacaccaattcagaaaagtattctaattgg-ctagctaagctttaactgccttcatgagcgatgct-----gacttgttcccttcgttgttgtttggtaacagGTACTTATATTGATAAGAAATGCCCCTTCACTGGCACTGTTTCTATTAGGGGCCGCATCTTAGCTGGCACTTGCCATAGTGCCAAGATGATGAGGACCAT

upper sequence: GLYMA09G12430.1 (Glycine max), 3'ss of exon 3
lower sequence: EDO96718 (Chlamydomonas reinhardtii), 3'ss of exon 2
-------------------------------------------aaccttcaccttcactattccatttgggctacattttcttctgtctatttggtgacttctgtttctaaatcatggtcctgttttttttccccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
                                           || | |        |       |   |    |        | | |      |    ||  ||        ||    || |   |  ||| |  | | ||||   ||| || |||||||||||||||||||| ||||| || ||||| || || ||||||||  | |                                  
gtgcgtcccggggagctttgcgctaaacgtaatggagtaaataaatcgtgtggcaggcagggttgtgccgtgggcgccgcacgccggcagcgccgacgattgagtgcgcggtccaataaccaggcgtgcttcactgcctgcagGCCACTACATCGACAAGAAGTGCCCCTTCACCGGCAACGTGTCCATCCGTGGCCGTATCCTCACGG----------------------------------

upper sequence: GLYMA09G12430.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S21_269V6.1 (Physcomitrella patens), 3'ss of exon 3
----aaccttcaccttcacta--ttccat--ttgggctacattttcttctgtctatttggtgacttctgtttctaaatcatggtcctgttttttttccccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
      | |  || |  | ||  | |||   |||   ||   |||  | ||  | ||  ||||  |||||    | |||  ||   |||| |         | | |||| ||||| ||||||||||||||||| ||||| ||  |||| |||||||| || || |||||| | || |||    || |  | ||||||||  | |||||
ttcatgcttagacgtaaaataaatcccaaggttgcattagggtttgatgtgaatgttgagtga--tctgtgctgagatctcgggagtgttctaaa------ctttcagGCACCTACATTGACAAGAAGTGCCCATTCACCGGAGATGTCTCCATTCGAGGCCGCATCCTAACTGGAACTGTGAACTGCACCAAGATGACTCGCACCAT

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|58021442|gb|CX708183.1|CX708183
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|298185405|gb|HO030618.1|HO030618
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|58025331|gb|CX712072.1|CX712072
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|7926332|gb|AW832358.1|AW832358
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|31466051|gb|CD408079.1|CD408079
EST:     TGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGTATGCCATTGAAG                         GTACCTATATTGACATAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGG
genomic: TGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAG-ATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACA-AGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGG
EST: gi|298198041|gb|HO039580.1|HO039580
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|298199106|gb|HO042469.1|HO042469
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTAACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|31476512|gb|CD418540.1|CD418540
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCCATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|13181115|gb|BG352455.1|BG352455
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|192303094|gb|FG994212.1|FG994212
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|31309567|gb|CD394770.1|CD394770
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|298171592|gb|HO021184.1|HO021184
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|120532484|gb|EH260617.1|EH260617
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|31461828|gb|CD403856.1|CD403856
EST:     TGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|298195925|gb|HO044316.1|HO044316
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|15336926|gb|BI497582.1|BI497582
EST:     TTGGAAGTCAATTGGGCTTGGATTCAATATTCTCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|58014715|gb|CX701457.1|CX701457
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|298163527|gb|HO012260.1|HO012260
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|11414033|gb|BF425973.1|BF425973
EST:     TGGAAGTCAATTTGGGCTGGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TGGAAGTCAA-TTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|151404874|gb|EV274688.1|EV274688
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|31464691|gb|CD406704.1|CD406704
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttggtgacttctgtttctaaatcatggtcctgttttttttccccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
                 ttctaaa  putative branch site (score: 2)
                              tcctgttttttttccc  putative PPT
                                 tgtttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaccttcaccttcactattccatttgggctacattttcttctgtctatttggtgacttctgtttctaaatcatggtcctgttttttttccccccatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- -cttcacc
- - - - - - - - - -ccatttg
- - - - - - - - - - - - - - ctacatt
- - - - - - - - - - - - - - - - - - - ttctgtc
- - - - - - - - - - - - - - - - - - - - - - - - -tggtgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttc