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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacgttgcttaccttaaaaagataccaataatatggtcatagtgaaagacaagtgacttattaattcctccggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTGACTGGGGAGAGCTTAGACTCTAGAGGCCTTTATATTTATGATGATGGTT

Basic information

species Glycine max
transcript GLYMA03G38830.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38830.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv19s0014g01900.t01 (Vitis vinifera), 3'ss of exon 11
----gtatacgttgcttaccttaaaaagataccaataatatggtc-atagtgaaagacaagtgacttattaattcctccggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTGACTGGGGAGAGCTTAGACTCTAGAGGCCTTTATATTTATGATGATGGTT------------
        |  |   ||   || ||      ||||| ||    |  |    |  |  |     |  |     | | |    | || ||| || |||  ||||| |||||| |            || |||||||||  |   || |||||||||||| |||||||| || |||||||||||||||||||            
gtaaaggaatttcttttggtttgaattttctccaatcatgccttttactacgtgaatctctaaaactgcatctacatgtcatattgcagCCAACTGCTCAGGCAGATGAGTT------------GAAAAGGTTACCACTAGTTGCGGAGAGCTTAGATTCTAGAGGTCTATATATTTATGATGATGGTTTTCGCTTTGTTA
















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|16347425|gb|BI973020.1|BI973020
EST:     TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAG                         GCATCTGTACAGGCTGATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
genomic: TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAGgtatacgttg ... ggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTG
EST: gi|6072200|gb|AW101587.1|AW101587
EST:     TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAG                         GCATCTGTACAGGCTGATGACTTANAAAGTGTTGAGAGAAGGTTACCTTTG
genomic: TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAGgtatacgttg ... ggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTG
EST: gi|16105691|gb|BI893431.1|BI893431
EST:     TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAG                         GCATCTGTACAGGCTGATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
genomic: TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAGgtatacgttg ... ggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTG
EST: gi|17400168|gb|BM176950.1|BM176950
EST:     TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAG                         GCATCTGTACAGGCTGATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
genomic: TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAGgtatacgttg ... ggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTG
EST: gi|17153026|gb|BM142959.1|BM142959
EST:     TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAG                         GCATCTGTACAGGCTGATGACTTAAAAAGTGTTGAGAGA
genomic: TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAGgtatacgttg ... ggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGA
EST: gi|15001174|gb|BI321988.1|BI321988
EST:     TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAG                         GCATCTGTACAGGCTGATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
genomic: TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAGgtatacgttg ... ggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTG
EST: gi|7588638|gb|AW704429.1|AW704429
EST:     TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAG                         GCATCTGTACAGGCTGATGACTTAAAAAGTGTTGAGAGAAGGTTACCTTTG
genomic: TGAAACTTCTCTATCCTAGCTTAATTCGACTTGATGAATATCTTCTGAAGgtatacgttg ... ggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatatggtcatagtgaaagacaagtgacttattaattcctccggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTGACTGGGGAGAGCTTAGACTCTAGAGGCCTTTATATTTATGATGATGGTT
                                tattaat  putative branch site (score: 2)
                                      ttcctccg  CT-rich tract
                             acttattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacgttgcttaccttaaaaagataccaataatatggtcatagtgaaagacaagtgacttattaattcctccggtgttccagGCATCTGTACAGGCTGATGAGGTACAAAGTGTTGAGAGAAGGTTACCTTTGACTGGGGAGAGCTTAGACTCTAGAGGCCTTTATATTTATGATGATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT