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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttctgtttttagcatttgccatttttataatttttccagttttcccagttaatttttgatgcattttctggttgcttggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAATTATATAGCTCTGTCAG

Basic information

species Glycine max
transcript GLYMA12G37100.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 19
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 19
-------------------------gtaagcttctgtttttagcatttgccatttttataatttttccagttttcccagttaatttttgatgcattttctggttgcttggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAATTATATAGCTCTGTCAG
                         | |||||     ||||    |    |  |||| |   ||    || || | | || |   |   | ||  | |    |  |    |  |||||| ||||| ||||||||||| || || || ||||||||||||||||||||| | || || ||| | ||
gtgaactatccttatgcaaaagctcgaaagctctaaattttcttgtccatctcttttct--cttacagagattcctcggtcatgctactaagcgatgtgaattgacc--atgaacagGCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAG

upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
gtaagcttctgtttttagcatttgccatttttataatttttccagttttcccagttaatttttgatgcattttctggttgcttggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAATTATATAGCTCTGTCAG
||||||   |||   |   | ||  |||||||  |  ||| |   | |   || |||     || |  | | | || | | ||||||  ||||||||||| ||||| |||||||| || ||||||||||||||||| ||||| || || |||||  ||||
gtaagcacttgtccctg--aattctcatttttgcatctttac--atctggtcactta-caaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
















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|298194073|gb|HO040721.1|HO040721
EST:     GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAG                         GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
genomic: GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAGgtaagcttct ... tggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
EST: gi|13312451|gb|BG406102.1|BG406102
EST:     GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAG                         GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
genomic: GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAGgtaagcttct ... tggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
EST: gi|9564156|gb|BE473665.1|BE473665
EST:     GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAG                         GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
genomic: GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAGgtaagcttct ... tggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
EST: gi|18038693|gb|BM306987.1|BM306987
EST:     GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAG                         GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
genomic: GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAGgtaagcttct ... tggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
EST: gi|209705823|gb|BW675928.1|BW675928
EST:     GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAG                         GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
genomic: GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAGgtaagcttct ... tggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
EST: gi|151401960|gb|EV271773.1|EV271773
EST:     GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAG                         GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
genomic: GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAGgtaagcttct ... tggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
EST: gi|51336285|gb|CO980151.1|CO980151
EST:     GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAG                         GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
genomic: GTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAGgtaagcttct ... tggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
EST: gi|254322389|gb|GR837803.1|GR837803
EST:     GTTTAGCTGCTAATGTTCCAAAG                         GCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA
genomic: GTTTAGCTGCTAATGTTCCAAAGgtaagcttct ... tggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccagttttcccagttaatttttgatgcattttctggttgcttggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAATTATATAGCTCTGTCAG
                      ttttgat  putative branch site (score: 4)
               agttaatttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttctgtttttagcatttgccatttttataatttttccagttttcccagttaatttttgatgcattttctggttgcttggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAATTATATAGCTCTGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG