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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgactaatgtcttagttcctctgtatctcttgctaattttctttttactgtgattaattctctcttgcttctttctttttattgtgtcgtttaaatggttttcatttgatcgctgctccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTGACATCGGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC

Basic information

species Glycine max
transcript GLYMA08G45270.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 14
gtaagtgactaatgtcttagttcctctgtatct-cttgctaattttctttttactgtgattaattctctcttgcttctttctttttattgtgtcgtttaaatggttttcatttgatcgctgctcct-tttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTGACATCGGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
                         |||||  | |||||||  ||     |||    |     ||| || ||  |   |     ||  |    | || |  |       |    |  | ||    | || ||||| ||  |||| |||||||||||  |||| || ||||||||| | ||||| |||||||| || || ||| ||||| ||||||| |||||||| ||||| |
-------------------------ctgtacatgcttgctatgttggaacttatcacg-----ttcgctgttattgtgtggcggttgata-accattgagcttaccacaaa--aactgttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 13
gtaagtgactaatgtcttagttcctctgtatctcttgctaattttctttttactgtgattaattctctcttgcttctttctttttattgtgtcgtttaaatggttttcatttgatcgctgctccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTGACATCGGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
                            | | | |    |   |  |||  |   | |||   |    | || |    | ||  |     || |||  ||    | | | | |   |  |  |  || ||||| ||  |||| ||||||||||| ||||| || || || ||||| ||||| || || ||||||||||||   ||| | ||||| |||||||||||| |||
------------------------atgatgtgtgtaatcagactcattt--atcatcattg--ttgtacatgatggcatgttagtgcatagtggttggaaa---tctaactcgtcggtggtactcttacagGCGCCCCAAGGAGTGCATGTGGTGTGCAAGAGATTCCCTAGAATGAAGATCGTTACTTCGGAGATTGAGTCCGGTCTAAATGATGATTTCCGTGTCGTAC

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G26510.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaagtgactaatgtcttagttcctctgtatctcttgctaattttctttttactgtgattaattctctcttgcttctttctttttattg---tgtcgtttaaatggttttcatttgatcgctgctccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTGACATCGGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
                | || |       | |  ||||  ||  | | |  ||      | |||    |||     | | | |  |      ||  | |  | ||   |   |||  ||  || ||    |||||||||| ||||||| |||||||| |||||||  || ||||||||||||||||||||||| || || || | ||| || || ||||| || ||||| || |
---------------gtaagctaacacacaccctttgcgtatcatttatacaccccttgtgattactccttatccatgtttatccacaagaatgcagctggattgagatattttttttctttgttcaa--tcagGCACCTCAAGGTGTTCATGTGGTCTGCAAAAAATTCCCAAGAATAAAGATAGTGACATCTGAAATCGATAATGGGTTAAACGAAGAGTTTCGTGTTATTC

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 14
gtaagtgactaatgtcttagttcctctgtatctct-tgctaattttctttttactgtgattaattc--tctcttgcttctttctttttattgtgtcgtttaaa---tggttttcatttgatcg--------ctgctccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTGACATCGGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
|||||    |   | | | ||| || |   | | | |   |   ||    | | | | |  | ||     | | ||| || || ||    ||   |  |  |    || | ||||| |    |        ||    |||  ||||||||| | || ||||||||||| |||||||| || || || |||||||| || ||||| ||||||||  ||||| ||||||||||||||||||||||||
gtaagcccatgtagcccttgttgctattcgtttttgtatcacacttgaactcattataaaaagtttgacttttggctgctctccttcccatggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC

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|20811761|gb|BQ296239.1|BQ296239
EST:     TAAAAAAGGGTGTACCTGAGTCCAACATTATATTCCTTAATCTCATATCT                         GCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATA
genomic: TAAAAAAGGGTGTACCTGAGTCCAACATTATATTCCTTAATCTCATATCTgtaagtgact ... tccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATA
EST: gi|31311442|gb|CD396645.1|CD396645
EST:     TAAAAAAGGGTGTACCTGAGTCCAACATTATATTCCTTAATCTCATATCT                         GCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATA
genomic: TAAAAAAGGGTGTACCTGAGTCCAACATTATATTCCTTAATCTCATATCTgtaagtgact ... tccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATA
EST: gi|11412692|gb|BF424703.1|BF424703
EST:     GTCCAACATTATATTCCTTAATCTCATATCT                         GCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATA
genomic: GTCCAACATTATATTCCTTAATCTCATATCTgtaagtgact ... tccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATA
EST: gi|209716821|gb|BW654340.1|BW654340
EST:     TAAAAAAGGGTGTACCTGAGTCCAACATTATATTCCTTAATCTCATATCT                         GCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATA
genomic: TAAAAAAGGGTGTACCTGAGTCCAACATTATATTCCTTAATCTCATATCTgtaagtgact ... tccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATA
EST: gi|13240468|gb|BG359777.1|BG359777
EST:     TAAAAAAGGGTGTACCTGAGTCCAACATTATATTCCTTAATCTCATATCT                         GCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTNTCCAAGAATAAAGATA
genomic: TAAAAAAGGGTGTACCTGAGTCCAACATTATATTCCTTAATCTCATATCTgtaagtgact ... tccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttttattgtgtcgtttaaatggttttcatttgatcgctgctccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTGACATCGGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
                                atttgat  putative branch site (score: 5)
                                      tcgctgctccttttc  CT-rich tract
     ttttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgactaatgtcttagttcctctgtatctcttgctaattttctttttactgtgattaattctctcttgcttctttctttttattgtgtcgtttaaatggttttcatttgatcgctgctccttttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTGACATCGGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA