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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacctcaatttcacatctaataatgtgtttttgtttgcattattattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct...

Basic information

species Glycine max
transcript GLYMA08G23730.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 5'ss of exon 13
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacctcaatttcacatctaataatgtgtttttgtttgcattattattg--tttttgtatgaagtacatcctatcaaaagttagtttatttgttct----
||| || || ||||||||||||||||| ||||| ||| | ||||| || || ||||| ||||||||||||||||| || || || ||||| ||||  |||||||||     | ||||     | | |||  |  |   |  ||  |||   | ||     | || | |     |  | |      || |  |  |||| |||    
TCTTACGGGGAACAAAACATACCAAGACTGGGGGTGGGACATATTCCAGGCATTTGAAAAGAACTCCCGCATAGAATCTGGTTACGTTGGGCTGAGAGATgtaagctttttttaattgtttttatgata--gcatccatacttaaattcccactgagcgctagtgtaagacttacacaaattcttgtcaaatattttggtctccag

upper sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacctcaatttcacatctaataatgtgtttttgtttgcattattattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct
  | || || || |||||||||||||| ||||| ||| | ||||| || || ||||||||||||||||||||||| || || ||||| |||||||  |||||| | |  |||||   | || |||| |  ||  ||| || |          |    ||||| |||      | || |  ||  || |  | || |    
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtagg-attcctca---tgacttctattgttgaatttctgctga-------gtaacatttgtctgacaactgttct-tggaacatttgcct-ttag----

upper sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G128914_T01 (Zea mays), 5'ss of exon 13
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacctcaatttcacatctaataatgtgtttttgtttgcattattattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct
  | || || || | |||||||||||| ||||| ||| | ||||| || || |||||||||||||||||  |||| || || ||||| |||||||  |||||| |    |||||   | ||  | | | |||  ||| ||   | | ||  |||     ||| |||   |  |  | |   ||  |   |  |  |    
CTTGACGGGGAATACAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGTGTAGAATCTGGATATGTGGGACTGAGAGATgtaggttt-cctca---tgactcccattgatgaatttctgc--ggaataacatt-----tgtctgacacaactattgttggaacatttgtcttcag----

upper sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 5'ss of exon 13
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacctcaatt------tcacatctaataatgt----gtttttgt---ttgcattat-------tattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct---------------
  ||||||| ||||| ||||| ||||| ||||| |||||||||||| |||| |||||||||||||| ||||||||||| || ||||||||  |||||||||||||    ||  |         | | |||    | |||       || ||   ||| |||||        |   | | | |  | | |  |   || |  | | ||| || ||  ||||               
GTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag

upper sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 5'ss of exon 13
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagca-cacctcaatttcacatctaataatgtgtttttgtttgc-attattattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct---
  ||||||| ||||| ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||| |||| || || ||||| ||  |||||||||||||   |    |    | || |  |  |||  | |    |   | | |     | |   | | |     |||   | | ||  ||| | || ||  || |   
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaac-gtttgcttcttcattttcag

upper sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 5'ss of exon 8
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacc--tcaatttcaca----tctaataatgtgtttttg-tttgcattattattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct
| ||||||||| ||| ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||||| ||||   ||||  ||||      ||| |   |  |   || |||||||| ||| | |||   | |||| |        | |||  ||||   ||       
TTTAACTGGCAGCAAGACATACCAAGAGTGGGGTTGGAACATATTTCAAGCATTTGAAAAGAACTCCCGCATAGAGTCAGGATATGTTGGACTGAAGGATgtaagtacactcttcaaactcactaatccctacttcagactggctgatttgcatttttagtatttacttttgaactttgattcctgaaatcttagaacat-------

upper sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 5'ss of exon 13
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacc--tcaatttcaca----tctaataatgtgtttttg-tttgcattattattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct
| ||||||||||||| ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||||||||| || |||||||||||||||||||| ||||   ||||  ||||      ||| |   |  |   || || ||||| |||   |||   | |||| |        | |||  ||||   ||       
TTTAACTGGCAACAAGACATACCAAGAGTGGGGTTGGAACATATTTCAAGCATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacactcttcaaactcactaatccctacttcagactgactgattcgcatttttagcatttacttttgaactttgattcctgaaatcttagaaaat-------

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|10845781|gb|BF068830.1|BF068830
EST:     GCATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: GCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
EST: gi|17020914|gb|BM091948.1|BM091948
EST:     CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
EST: gi|120494883|gb|EH223050.1|EH223050
EST:     CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
EST: gi|208258043|gb|GE050990.1|GE050990
EST:     CTTTTGAGAAGAACTCCCGGATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
EST: gi|22932226|gb|BU549365.1|BU549365
EST:     CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
EST: gi|192311621|gb|FK003104.1|FK003104
EST:     CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
EST: gi|27445891|gb|CA953014.1|CA953014
EST:     CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
EST: gi|120529222|gb|EH257356.1|EH257356
EST:     CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
EST: gi|151407654|gb|EV277469.1|EV277469
EST:     CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
EST: gi|192311620|gb|FK003103.1|FK003103
EST:     CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGAT                         GTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG
genomic: CTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacac ... catttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacctcaatttcacatctaataatgtgtttttgtttgcattattattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG