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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgatgatttctgggactttgaagtcttgatttgagagatgttgtggctcattgtgtggcaatttgaacgttttatctgggggttcaactttgccctttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG

Basic information

species Glycine max
transcript GLYMA20G24830.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G058702_T01 (Zea mays), 3'ss of exon 4
gttagtgatgatttctgggactttgaagtcttgatttgagagatgttgtggctcattgtgtggcaatttgaacgttttatctgggggttcaactttgccctttatt---tccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG
                               ||   | |      ||    |  | | | ||  || |  ||  | | ||     | || |  || |    | | |   | ||||| ||||| ||||||||||| || || || ||||| ||| |||||||||||||||| ||||| ||||| ||||  |||||||||
------------------------------gtgggcttacttccttttcttcctagtctatgtaaactgtaatatgt-atacaaagattaatattcgagtatcaatgagtgcagGGAGCTATTATGGCTGTTGGAGCCTCGAAACCTACAGTTGTGGCTGATAAAGATGGTTTCTTTAGCGTCAAGAGCAAAATGCTG

upper sequence: GLYMA20G24830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G117786_T01 (Zea mays), 3'ss of exon 4
gttagtgatgatttctgggactttgaagtcttgatttgagagatgttgtggctcattgtgtggcaatttgaacgttttatctgggggttcaactttgccctttatt---tccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG
                | |   || ||  |||   ||   |||   |||      |    ||     ||   |  | | | || ||||| |  ||||    | | |   | ||||| ||||| ||||||||||| || || || ||||| ||| |||||||||||||||| ||||| ||||| ||||  |||||||||
----------------gtgggcttaaatccttttcttcctagaccatgtaaactgtaaaatgtatgcttc--ccatatgtatgagggttaatatttgagtatcactgagtgcagGGAGCTATTATGGCTGTTGGAGCCTCGAAACCTACAGTTGTGGCTGATAAAGATGGTTTCTTTAGCGTCAAGAGCAAAATGCTG

upper sequence: GLYMA20G24830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G121200_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------gttagtgatgatttctgggacttt-----gaagtct--tgatttgagagatgttgtggctcattgtgtggcaatttgaac-gttttatctgggggttcaactttgccct-ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG
                                               |||  |     | | ||||  | |     |  ||||  || ||    || |  | ||     |||  | | | | |   |  ||||||          ||  ||||    |||| | ||||| ||||||||||||||||| || ||||  ||||||||  |||||||||| ||||| ||||| ||  | |||| | ||||||||
gtgggtttcttccctggtgtatgttgtctgtccagttagtatgaaatgttgatagaattgtatgggtttcttccctggtgtctgatgtttgtctagttagtatgaaatgttg-atagaattgtattctattttattaaacacaagaagattgcatggttatatgcagGGGGCTATCATGGCTGTTGGAGCGTCAAGACCTACTGTAGTGGCTGATAAGGATGGTTTCTTTAGTATCAAGAGTGAAATGCTG

upper sequence: GLYMA20G24830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G25860.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagtgatgatttctgggactttgaagtcttgatttgagagatgttgtggctcat-tgtgtggcaatttgaacgt-tttatctgggggttcaactttgccctttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG
                            | |  |    |      |||   ||  | ||  | |  |||  || |  ||||  |    |||  |||         || || |||||||||| ||||||||||| || |||||||| |||||  | |||||||| |||||||||||||| || || || | |||||||
-------------------------gtatatgaaagaaactttcattgcctcttctatgaatagtgattacaaggaatttacttaattgttatactcaa------atctctagGGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTG

upper sequence: GLYMA20G24830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 4
gttagtgatgatttctgggactttgaagtct--tgatttgagagatgttgtggctcattgtgtggcaatttgaacgttttatctgggggttcaactttgccctttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG
|| |||    |   |  ||||||| |  |||  |  ||    ||||  |   || | ||   |||  || ||   | ||| |||     ||     |          |  ||||| ||||||||||| ||||| || ||||||||||||||| |  |||||||||||||||||||||| || || | ||||||||||
gtgagttgcaaagcc-aggactttcacctctattagttcataagattcttctgcccttt---tgggcatgtgtgagctttttctcaaaatttggaatga--------tgtcagGGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG

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|208134819|gb|GD930022.1|GD930022
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGACGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCT
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCT
EST: gi|207747462|gb|GD720223.1|GD720223
EST:     CCATACTTCCGCCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
genomic: CCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
EST: gi|19053677|gb|BM732344.1|BM732344
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
EST: gi|9985549|gb|BE659657.1|BE659657
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
EST: gi|6134907|gb|AW133300.1|AW133300
EST:     GGGTATGTNTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
genomic: GGGTATGT-TTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
EST: gi|22525077|gb|BU083888.1|BU083888
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTC
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTC
EST: gi|7478035|gb|AW666112.1|AW666112
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
EST: gi|14011336|gb|BG726189.1|BG726189
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
EST: gi|31464480|gb|CD406508.1|CD406508
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
EST: gi|18735643|gb|BM528886.1|BM528886
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
EST: gi|208054335|gb|GD854472.1|GD854472
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGG                         GGTGCTATCATGGCTGGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATA
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCA-Ggttagtgatg ... ttatttccagGGTGCTATCATGGCT-GTTGGCGCATCAAAGCCTACTGTTCTGGCTGATA
EST: gi|31466163|gb|CD408191.1|CD408191
EST:     TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG                         GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA
genomic: TGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatg ... ttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtggcaatttgaacgttttatctgggggttcaactttgccctttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG
                                    ctttgccctttatttc  CT-rich tract
                                            tttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgatgatttctgggactttgaagtcttgatttgagagatgttgtggctcattgtgtggcaatttgaacgttttatctgggggttcaactttgccctttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG