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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacttgtacaggagtcatttagattgtattttgatttgttcatagtcgtccgtacttatcagttctctcttaaccaacaaagatacatttgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTCGGAGATGGATCAACAAGTCTATTTTTTCAGTTG

Basic information

species Glycine max
transcript GLYMA04G40220.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40220.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G061980_T01 (Zea mays), 3'ss of exon 7
--tgacttgtacaggagtcatttagattgtattttgatttgttcatagtcgtccgtacttat--cagttctctcttaaccaacaaagatacatttgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTCGGAGATGGATCAACAAGTCTATTTTTTCAGTTG
  |    | |  | |  | |||  | ||| |||    ||||  | |  || |||   || ||  ||         | ||  |     ||     ||||| | ||||| ||| |||| || ||||| || || ||||| |||||||||||||| |||||| | ||| | || || ||||| || ||||||||||| || ||||||
ggtagtatctcaatgcttaatt--gtttgcattact-tttgcccgtgatcctcctatctaataacaaacgagaagtgactgattgctattatgctgtttct-agGTTCGAGCGAGAGCGGACTTGCCCCTTGTGCAGAGCATTGGTAAAACCTGCTGATATCCGGTCATTTGGTGATGGTTCTACAAGTCTATTCTTCCAGTTG

upper sequence: GLYMA04G40220.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ13527 (Selaginella moellendorffii), 3'ss of exon 7
tgacttgtacaggagtcatttagattgtattttgatttgttcatagtcgtccgtacttat-cagttctctcttaaccaacaaagatacatttgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTCGGAGATGGATCAACAAGTCTATTTTTTCAGTTG
              ||   ||  ||   ||  |    ||| ||  |  |    |  | || |   | | ||||                |||| |   |||||||||||| || |||||||||||||||||  |  |  | || ||  |  | || ||  |  | || || ||||| || || ||||| ||| | ||| | 
--------------gtacgtttcatcaaatcct---ctgtgcaagggagagaattttcatgcgagtttttcttcgtt------------tttgctacacagGTTTGAGAGGGAGCGAACTTGTCCATTATGTCGATCGGTTGTGAAGTCGTCGGAGCTAAGATCTTTTGGCGATGGCTCCACGAGTCTCTTTGTACAGCTC

upper sequence: GLYMA04G40220.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ19091 (Selaginella moellendorffii), 3'ss of exon 7
tgacttgtacaggagtcatttagattgtattttgatttgttcatagtcgtccgtacttat-cagttctctcttaaccaacaaagatacatttgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTCGGAGATGGATCAACAAGTCTATTTTTTCAGTTG
              ||   ||  ||   || ||    ||| ||  |  |    |  | |  |   | | ||||                |||| |   |||||||||||| || |||||||||||||||||  |  |  | || ||  |  | || ||  |  | || || ||||| || || ||||| ||| | ||| | 
--------------gtacgtttcatcaaatctt---ctgtgcaagggagagaattttcacgcgagtttttcttcgtt------------tttgctacacagGTTTGAGAGGGAGCGAACTTGTCCATTATGTCGATCGGTTGTGAAGTCGTCGGAGCTAAGATCTTTTGGCGATGGCTCCACGAGTCTCTTTGTACAGCTC

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|151406003|gb|EV275818.1|EV275818
EST:     ATATTGTTGAGCTGTAA-CACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|207809978|gb|GD781492.1|GD781492
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|22525728|gb|BU084539.1|BU084539
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|22525809|gb|BU084620.1|BU084620
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|31307902|gb|CD393105.1|CD393105
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|151404475|gb|EV274289.1|EV274289
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|209698400|gb|BW667195.1|BW667195
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
EST: gi|16343713|gb|BI969308.1|BI969308
EST:     ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATG                         GTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC
genomic: ATATTGTTGAGCTGTAAACACATGTTCTGTGAGGAGTGTGTATCTGAATGgtcagttaat ... tgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgtccgtacttatcagttctctcttaaccaacaaagatacatttgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTCGGAGATGGATCAACAAGTCTATTTTTTCAGTTG
                       tcttaac  putative branch site (score: 2)
                                           tttgtttttc  putative PPT
                                      atacatttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacttgtacaggagtcatttagattgtattttgatttgttcatagtcgtccgtacttatcagttctctcttaaccaacaaagatacatttgtttttcagGTTTGAGAGAGAACGAACTTGTCCATTATGCAGGGCATTGGTAAAACCAGCTGATCTGCGGACCTTCGGAGATGGATCAACAAGTCTATTTTTTCAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
tgacttg
- - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacaa