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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttattttttatgataagattcaattcattttttgctccttgttttatttcctgttctctaatgttcctcagttttgcttgcttcctttctattcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATGGTTACTGATGAGGTAGAGCTTCAGCAACATCAGAAACTTGAGAAGCTTT

Basic information

species Glycine max
transcript GLYMA04G01100.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 1
tttgttattttttatgataagattcaattcattttttg--ctccttgttttatttcctgttctctaatgttcctca------gttttgcttgcttccttt----ctattcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATGGTTACTGATGAGGTAGAGCTTCAGCAACATCAGAAACTTGAGAAGCTTT
             ||||    |||  | |  | || ||  |||| |  ||||| | ||| | | ||||  |  ||       ||| || |   ||| ||      ||  |||||||| || ||||||||||| | ||||||||| || || ||||||||| |  |||||||||||| |||||||||||| |||||||||||||| |||||||
------------catgaattcatttcacttctgttgtggtctccatactttatgtgctgatttttaataattttcttgagatgttgtgttaatttcattgaatattacacagGCTGTCCTCAAACAGTTTGGTGGTGGGGGATACGGGGGTTCAGATAATGTAATTACTGATGAGGCAGAGCTTCAGCAGCATCAGAAACTTGAAAAGCTTT

upper sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 1
tttgttattttttatgataagattcaattcattttttgc-----tccttgttttatttcctgttctctaatgttcctcagttttgcttgcttcctttctat-tcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATGGTTACTGATGAGGTAGAGCTTCAGCAACATCAGAAACTTGAGAAGCTTT
     |  | | |||| | | | |   |  | | | | |     ||   | |||| ||  ||  || |  ||    | |   ||| | | |   |||  ||  |||||||| || || ||||||   | ||| || ||||| ||  |||||||| |  | |||||||||  ||| |||||||||||||| ||||||||||| ||||
----ctcgtctctatggttatactttttcaaatgtatacgagtttctgaggtttacttggtgg-ctttgctgaaaattatgattgat-gttgaattttgatgccagGCTGTTCTCAAGCAGTTTTCTGGTGGTGGTTATGGTGGCCCAGATAATGTCCTCACTGATGAGTCAGAACTTCAGCAACATCAAAAACTTGAGAAACTTT
















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|24136864|gb|BU927374.1|BU927374
EST:     TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAG                         GCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATG
genomic: TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAGgttccttcaa ... ttctattcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATG
EST: gi|18039567|gb|BM307861.1|BM307861
EST:     TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAG                         GCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGTTCAGATAATATG
genomic: TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAGgttccttcaa ... ttctattcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATG
EST: gi|298187568|gb|HO034717.1|HO034717
EST:     TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAG                         GCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATG
genomic: TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAGgttccttcaa ... ttctattcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATG
EST: gi|5126412|gb|AI748148.1|AI748148
EST:     TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAG                         GCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATG
genomic: TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAGgttccttcaa ... ttctattcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATG
EST: gi|16347039|gb|BI972634.1|BI972634
EST:     TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAG                         GCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATG
genomic: TCAGAAAGCAAGCCTCCAAACTTCGAGAACAGGTCGCTCGTCAACAACAGgttccttcaa ... ttctattcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatttcctgttctctaatgttcctcagttttgcttgcttcctttctattcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATGGTTACTGATGAGGTAGAGCTTCAGCAACATCAGAAACTTGAGAAGCTTT
              ctctaat  putative branch site (score: 3)
                      ttcctcagttttgctt  CT-rich tract
                                            tttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttattttttatgataagattcaattcattttttgctccttgttttatttcctgttctctaatgttcctcagttttgcttgcttcctttctattcagGCTGTGCTTAAACAGTTTGGGGCTGGGGGATATGGAGGATCAGATAATATGGTTACTGATGAGGTAGAGCTTCAGCAACATCAGAAACTTGAGAAGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - caattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgct