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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTGCTAGCATTAAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtcttaagcttagtctcagttaactccgctagataatctgttactattgaaccaccttatggaaaattatgatccaagtgtgcttttgactgttgtcag

Basic information

species Glycine max
transcript GLYMA19G30580.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30580.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 22
GACTTGCTAGCATTAAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtcttaagcttagtctcagttaactccgctagataatctgttactattgaaccaccttatggaaaattatgatccaagtgtgcttttgactgttgtcag
||| |||| ||| | |||||  | || || ||| | || |||| |||||| |||||||||||||| || || |||||||| ||||||||||||||| ||||        | | | | |||  | |  |   | |||    | ||   |   |   ||   ||| | |  |    | |  ||| ||   ||   | | 
GACCTGCTTGCACTTAAAGACAAGTACACCACAAGACCAGCAAAAGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaattttccaatatta-ttattttccttgcttcatcaaa-attaggtattaagagtaaacaaattcaaaaagagaattggctattc-ttgacataat

upper sequence: GLYMA19G30580.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 12
GACTTGCTAGCATTAAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtcttaagcttagtctcagttaactccgcta---gataatctgttactattgaaccaccttatggaaaattatgatccaagtgtgcttttgactgttgtcag
||| | || ||| | |||||  | || || ||| | || ||  ||||||| |||||||||||||| || || || ||||||||||||||||||||| ||||  ||  |   ||   ||  ||  |  ||    ||||   |||   | | |   | ||  |  ||  |||   | ||| |||    ||   | | |    
GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtc--aatttccatcattgtccacctctttatgaaataagacgttttcaataataaaactattttaatgttactcttcaaatgtcgccttctttttag----

upper sequence: GLYMA19G30580.1 (Glycine max), 5'ss of exon 23
lower sequence: AT2G40840.1 (Arabidopsis thaliana), 5'ss of exon 22
GACTTGCTAGCATTAAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtcttaa--gcttagtctcagttaactccgctagataatctgttacta--ttgaaccaccttatggaaaattatgatccaagtgtgcttttgactgttgtcag
||  || | ||  | |||||||| || || || || |||||||||||||||||||||||||| || || || || || ||||| ||||||| |||| ||| || |   || | |  ||   ||| |    |  ||  |   |  ||  ||  ||    || ||   |  ||                              
GATATGATGGCTCTGAAAGAAGAGTACACTACTCGTCCTGCAACAGAGGAGACAATCAATGATCCAACAAACCCCAAACACTACTGGAGATACCgtaagtatttactactaactaacacacaaccctaagaactataccagttttaacttagactgttttttgtgcatatag-----------------------------

upper sequence: GLYMA19G30580.1 (Glycine max), 5'ss of exon 23
lower sequence: Vv08s0040g00670.t01 (Vitis vinifera), 5'ss of exon 21
GACTTGCTAGCATTAAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtcttaagcttagtctcagttaactccgctagataatctgttactattgaaccacctt-atggaaaattatgatccaagtgtgcttttgactgttgtcag
|||||||||||| | ||| ||||||| ||||||||||||||| ||||||||||||| ||||| || || ||||| |||||||||||| ||| ||||  ||   ||  ||| |   | || ||||  ||      |       |    |    | |  |    |||||||  |||  || |  | |    |||  ||| 
GACTTGCTAGCACTGAAAAAAGAATACACAACACGCCCTGCAGCAGAGGAGACAATTAATGATCCCACAAATCCAAAGCACTATTGGCGATACCgtatgtacaaattttaat---attttactcaactgccgtgtgcacgcatgcaaacgtgcttagacatcaaattatcttcct-gttttatatcatgtgtgttcac

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|213589467|gb|DB981229.1|DB981229
EST:     AGAGGAGACAATCAATCAGCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTTGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|15203232|gb|BI426000.1|BI426000
EST:     AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|214010081|gb|DB989453.1|DB989453
EST:     AGAGGAGACAATCAATGACCCTACGGCCCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTGAGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|6725673|gb|AW310072.1|AW310072
EST:     AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|120491607|gb|EH219774.1|EH219774
EST:     AGAGGAGACAATCAATGGCCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|6725163|gb|AW309562.1|AW309562
EST:     AGAGAAGACAATCTATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|21675570|gb|BQ627921.1|BQ627921
EST:     AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|22524316|gb|BU083127.1|BU083127
EST:     AGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|13790804|gb|BG653395.1|BG653395
EST:     GAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: GAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|209699503|gb|BW682994.1|BW682994
EST:     AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|207756104|gb|GD727003.1|GD727003
EST:     AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|214007743|gb|DB986109.1|DB986109
EST:     AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|120491903|gb|EH220070.1|EH220070
EST:     ACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
genomic: ACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAATCATTGATCAAGGATAATGACCTCCAAACCA
EST: gi|18732935|gb|BM527331.1|BM527331
EST:     AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC                         GTGTGCATGTGACTTTGGAAT
genomic: AGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtctta ... ctgttgtcagGTGTGCATGTGACTTTGGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTTGCTAGCATTAAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtcttaagcttagtctcagttaactccgctagataatctgttactattgaaccaccttatggaaaattatgatccaagtgtgcttttgactgttgtcag

- - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT