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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttaaaattcaacaattcattgttcagctaaatacacatgtaaatttcattctgtgtacttgttttgttattaggacttatattctagggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTTTTATCATGGAAGGGCTAAACAAGCAGCAACCAGCACTTGCAGTTCCCAT

Basic information

species Glycine max
transcript GLYMA02G46620.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46620.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26670.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------ttgttaaaattcaacaattcattgttcagctaaata-cacatgtaaatttcattctgtgtactt-gttttgttattaggacttatattctaggg----ttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTTTTATCATGGAAGGGCTAAACAAGCAGCAACCAGCACTTGCAGTTCCCAT
              || |    ||||     |  | | |   | ||  || || ||  ||  | || ||     |    |    | || |||    | | || || ||    |||||||||||| ||||| |||||||| ||||| |||||||| ||||||||||| ||||||||  | || || || |||||    ||| ||||  | |||    |  |
gtaatccaaatccattatgctcattctgatttctactttggcgttatgtatcatatcaaagatgcaatcatcacagagaggagagctaatagattctttcttatatggccttttttacagGTGCTCCACAGGCTCTTCTACAGAGTTGTCTCACGTTTGGGGCATTCTCTTTTATTCTTGAGGGACTCAACAAAAGACAAACAGCTTTGGCACACTCGGT

upper sequence: GLYMA02G46620.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0090g01590.t01 (Vitis vinifera), 3'ss of exon 4
ttgttaaaattcaacaattcattgttcagctaaatacacatgtaaatttcattctgtgtacttgttttgttattaggacttatattctagggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTTTTATCATGGAAGGGCTAAACAAGCAGCAACCAGCACTTGCAGTTCCCAT
       | || ||||  |  ||| | || | | ||||   |    | |||  || |  | |||     |  ||  |    ||||      |||||  |||| ||||||| |||||||| ||||||||  ||||||||||||  || || |||||||| |||||||| ||||||||||| ||||| ||||||  |||  |
-----gtacttaaacatctggttgat-agattactacaagggc---tatcaacctattaaattgaggcttacttgtgctacatat------gttttgtagGTACACCACAGGCTCTTCTACAGAGCTGCGTCACTTTTGGGGTGTTCTCATTTATCATTGAAGGGCTTAACAAGCAGCAGCCAGCCCTTGCACATCCATT
















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|23727058|gb|BU761545.1|BU761545
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|17153736|gb|BM143669.1|BM143669
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|31468894|gb|CD410922.1|CD410922
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGCTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|26047850|gb|CA784505.1|CA784505
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|298181833|gb|HO026008.1|HO026008
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|298174609|gb|HO017832.1|HO017832
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|9898882|gb|BE607850.1|BE607850
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|22525642|gb|BU084453.1|BU084453
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|298184523|gb|HO029736.1|HO029736
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGCTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|31311953|gb|CD397156.1|CD397156
EST:     TAATGCGGCTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|31311320|gb|CD396523.1|CD396523
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|298178521|gb|HO024256.1|HO024256
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|298181875|gb|HO026050.1|HO026050
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|7925046|gb|AW831072.1|AW831072
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|6071305|gb|AW100692.1|AW100692
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|24135852|gb|BU926362.1|BU926362
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGGCTCACTTTTGGGGGATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|298173707|gb|HO017043.1|HO017043
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCCCTTCTGCAGAGCTGTCTCACTTTTGGGGCATCTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|15337011|gb|BI497667.1|BI497667
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|31459794|gb|CD401822.1|CD401822
EST:     GCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: GCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
EST: gi|18041339|gb|BM309633.1|BM309633
EST:     TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAG                         GTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT
genomic: TAATGCGGGTGTTGCTGGATGTTGCACTGGTCTTGCTCTAAGTTTTCCAGgtatctctta ... ggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcattctgtgtacttgttttgttattaggacttatattctagggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTTTTATCATGGAAGGGCTAAACAAGCAGCAACCAGCACTTGCAGTTCCCAT
                ttgttttgttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttaaaattcaacaattcattgttcagctaaatacacatgtaaatttcattctgtgtacttgttttgttattaggacttatattctagggttttacagGTGCACCACAAGCTCTTCTGCAGAGCTGTCTCACTTTTGGGGCATTTTCTTTTATCATGGAAGGGCTAAACAAGCAGCAACCAGCACTTGCAGTTCCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - caattca
- - - - - - - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg