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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatacttctttcttagattgtggtggttaatatgtcatacttattcgtttcgctggtcatctttttttccaactggctagtaaaatttcatccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG

Basic information

species Glycine max
transcript GLYMA08G22740.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G15840.1 (Arabidopsis thaliana), 3'ss of exon 4
--ctatacttctttcttaga---ttgtggtggttaat---atgtcatacttattcgtttcgctggtcatctttttttccaactggctagtaaaatttcatccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG
  | | | |   ||  ||||    |     |   | |   |||   |||||||      |       ||     | | ||| ||| || ||||          | ||||||| ||||| || ||||| ||||||||||| |||||||| || |||||||  ||| ||||||||||||| ||| | || |||||  | || ||||| ||
ttccaaattaaattagtagaaagctacatagaccagtcttatggagtacttata-acaacaaaaaaaatgaaaatattcaattggttactaaa-------tggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTAAGAAAGATCGAGGCAAAGCCGATTCTCCGATATACACTATGCAGATTTG

upper sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g06980.t01 (Vitis vinifera), 3'ss of exon 4
ctatacttctttcttagattgtggtggttaatatgtcatactt------attcgtttcgctggtcatctttttttccaactggctagtaaaatttcatccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG
        |   | |  | | ||||   ||||     | | |       |     |   | |   |     |||    | |  || ||  || |  |  | | ||||||| ||||||||||| || |||||||||||||| |||||||| ||||||| ||||   ||||| |||||||||   || |||||| | || ||||||||
------gcccaccatgaaatctggtaaataatgctatacattcgaacaaaccaaatcaacagaatagaaagtttgtttattaacttgttgaactgtacacttgcagGAGGATTTAATCAGCCCATCATGTGTGGTGGTGAACCAAGGGCAATGCTTAAAAAAGCCCGAGGAAAAGCTGATCGTCCCATATATACTATCCAGATATG

upper sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S99_42V6.2 (Physcomitrella patens), 3'ss of exon 4
ctatacttctttcttagattgtggtgg---ttaatatgtcatacttattcgtttcgctggtcatctttttttccaactggctagtaaaattt--catccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG
   |||  |  | | | | | || |     ||  |||||  |  |  | |   |      |||  |          ||  ||  | || |||    |  || |||| ||||||||||| || ||||||||||||||||||||  |    |||   |  ||  | || || |        |   | |||||| ||||  | |||  
--gtacaccaatatcaaactttgtttcccttttgtatgttttgttc-tgcacctttgcattcaggtgccacagaggct--ctgatcaagtttggtgttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGAAGAAGGAACGTGGAAGTCTATGCGAGACCATATATGCCATCAAAATAAA

upper sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S29_267V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------ctatacttctttcttagattgtggtggttaatatgtcatacttattcgtttcgctggtcatctttttttccaactggctagtaaaattt--catccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG
              ||  | | ||   || ||         ||  | || ||| |  || |     |    |||  |  | |    |   | |  |||||||   | |   | |||||||||| |||||||| |||||||||||||| |||||  |    |||   |  ||  | ||||| |    |    | || |||||||||||| | |||  
gtatactaagatcccttcattcctcctttggaagcacacccttcctttgacattcagatccacaatggcattcagatgctgtggagat--gttgataaaattggacgttggtgcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGAAGAAGGAACGAGGAAGCCTTTGCACTCCTATATATTCCATTAAAATAAA

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|9984428|gb|BE658536.1|BE658536
EST:     AGCTGCAACTCAACNNGTCNNNAATGAAGAANNNNNNATTGCTTTTAATG                         GAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
genomic: AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
EST: gi|22540175|gb|BU090018.1|BU090018
EST:     AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG                         GAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCC
genomic: AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCC
EST: gi|209725498|gb|BW677795.1|BW677795
EST:     AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG                         GAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
genomic: AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
EST: gi|17519754|gb|BM188796.1|BM188796
EST:     TTGGAATTGCTTTTAATG                         GAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
genomic: TTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
EST: gi|17519381|gb|BM188423.1|BM188423
EST:     AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG                         GAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
genomic: AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
EST: gi|17400692|gb|BM177474.1|BM177474
EST:     AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG                         GAGGTTTTAATCAGCCAA
genomic: AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAA
EST: gi|10232087|gb|BE800975.1|BE800975
EST:     AGCTGCAACTCAACTTGTCCCTAATGAAGAATCTGGAATTGCTTTTAATG                         GAGGTTTTAATCAGCCAATTATGTGTGG
genomic: AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAATTATGTGTGG
EST: gi|20448322|gb|BQ252446.1|BQ252446
EST:     AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG                         GAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
genomic: AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
EST: gi|151400172|gb|EV269986.1|EV269986
EST:     AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG                         GAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
genomic: AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
EST: gi|213608233|gb|DB970830.1|DB970830
EST:     AGCTGCAGCTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATG                         GAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA
genomic: AGCTGCAACTCAACTTGTCCCTAATGAAGAATTTGGAATTGCTTTTAATGgtaatttttg ... atccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtttcgctggtcatctttttttccaactggctagtaaaatttcatccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG
                                         tttcatcc  CT-rich tract
                                 tagtaaaatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatacttctttcttagattgtggtggttaatatgtcatacttattcgtttcgctggtcatctttttttccaactggctagtaaaatttcatccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - -tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggcta