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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttactattatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA

Basic information

species Glycine max
transcript GLYMA11G21490.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 3'ss of exon 6
tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttactattatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA
                    ||||  || |   | |      | | ||   | | |   ||||  ||||| | || |   |  ||   |    |  |||||||||||||||||||||||||||||| ||||| || |||   || ||| | || || |||   ||||| |||   || || ||| |
-------------------gtaattatgcaa-aatttacagatataccacatctcatgtttgatcctttgttaataaatctgataccctt---ttcttagGTTGAATGGGATGAGATAAATGCTGCTTGGGGTCAGGCTGCTCTTCTTTTGCATACCATGGCTCAGTACTTCACCCCAAAATTTGA

upper sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
-----------------------------tttatcctagagaattt--tcttaatcttgaactgaatcctttttcttcct--agtttgaatattgaagctttgattatgatgttactattatgaaa-----tgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA
                             |  || |   |   |||  |  |   |||||| |  || |    | | | |  | | |  || ||||  |||||  | | |||| || | | ||  |     |  |||||| || |||||||||||||||||||| |||||||| |||   || ||  | || || |||   ||||| |||   || || ||| |
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgt-taatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA

upper sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttactattatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA
                    ||||  |  ||||| | |        | ||| |  ||  |||   |  |      |  | | ||  ||   |||||  ||||||| |||||||||||||||||||| ||||| || |||   || ||  | || || |||   |||||||||   || || || ||
-------------------gtaattat--actgattgcaaaacg--catagatacaactttgtgtcactatactcggcgcttctgata-ataatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA

upper sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttactattatgaaa--tgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA
                   | | | |||        | | | | ||  || | |   | |    |||   ||| |  | | |  |  ||||||  | |||||||||| ||||||||||| |||||||| ||||||||||| || || || || || || |||||  | |||||||| || ||||||||
------------------gtaagttttgctactttccttgtatgtttataatctcgttct----gctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA

upper sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G61710.3 (Arabidopsis thaliana), 3'ss of exon 6
tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttactattatgaaa--tgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA--------------
                   | | | |||        | | | | ||  || | |   | |    |||   ||| |  | | |  |  ||||||  | |||||||||| ||||||||||| |||||||| ||||||||||| || || || || || || |||||  | |||||||| || ||||||||              
------------------gtaagttttgctactttccttgtatgtttataatctcgttct----gctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCAGTATCCTTATAACT

upper sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttact----attatg-aaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA
  |||   |   | |  | |  | |||    |  |    ||| |||  ||  ||| | | ||| ||   || || || |||  |    | | || |||  | ||||||||||||||||||||||||||||||||||||||||||||||| ||||| || || |||   || ||||||||||| ||||| ||
--tatgtcatcaactagtatacagcttattttagaatactttccttgata--ttgga-actgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA

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|58019925|gb|CX706667.1|CX706667
EST:     AGTTTGGAACAATTAACAATTTTCGACTTGGAAGACTTCCTAAAATTCCT                         GTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTT
genomic: AGTTTGGAACAATTAACAATTTTCGACTTGGAAGACTTCCTAAAATTCCTgtaagatgcc ... aaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTT
EST: gi|298194263|gb|HO040911.1|HO040911
EST:     AGTTTGGAATAATTAACAATTTTCGACTTGGAAGACTTCCTAAAATTCCT                         GTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTT
genomic: AGTTTGGAACAATTAACAATTTTCGACTTGGAAGACTTCCTAAAATTCCTgtaagatgcc ... aaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTT
EST: gi|57574660|gb|CX547635.1|CX547635
EST:     AGTTTGGAACAATTAACAATTTTCGACTTGGAAGACTTCCTAAAATTCCT                         GTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTT
genomic: AGTTTGGAACAATTAACAATTTTCGACTTGGAAGACTTCCTAAAATTCCTgtaagatgcc ... aaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTT
EST: gi|20498067|gb|BQ272997.1|BQ272997
EST:     AGTTTGGAACAATTAACAATTTTCGACTTGGAAGACTTCCTAAAATTCCT                         GTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTT
genomic: AGTTTGGAACAATTAACAATTTTCGACTTGGAAGACTTCCTAAAATTCCTgtaagatgcc ... aaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctagtttgaatattgaagctttgattatgatgttactattatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA
                    ctttgat  putative branch site (score: 5)
                                      tattatgaaatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttactattatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA

- - - - - - - - - - - - cttgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt