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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtgaaatactaattttggctgtttgaagagtcatagtttttacttattttagatcttgaacagatatatagtcatataactgttgttggttttgtagGTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTTAGCATGAACAAT

Basic information

species Glycine max
transcript GLYMA16G33080.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G101791_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------catgtgaaata--ctaattttggc----tgtttgaagagtcata-gtttttact----tattttagatcttgaacagatatatagtcatata--actgttg-----ttggttttgtagGTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTTAGCATGAACAAT
                                                 |  || |   |  || ||  |||     |||||  |||  |||    || || |    |||  |   |  | |  ||| |  |  ||| | |  ||||        ||  | |  ||||| |||||||| ||||| ||||| || || ||||| | ||||||||| |||||||||||  ||
gtatcacctgtatctactgtattttatctttcctaacatcatggtctgtcgagtaatgcacgcttatgctggtacattgtttagagaaacatgcacttatatttcaatatgattattacttattagagaacttctcacagagtactgacacaatcttattctgctagGTTCTCACTGAGCCAAAGAATGCCCTGGGTAAGCAATTCAAGAAATTGTTTAGCATGAATGAT

upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 11
-------------------------------------------------------------------------------------catgtgaaatactaattttggctgtttgaagagtcatagtttttacttattttagatcttgaacagatatatagtcatataactgttgttggttttgtagGTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTTAGCATGAACAAT
                                                                                      | |||| ||| |  ||       |  || |  |     |  || ||  | | | || |   |  | ||  || |   |    || | || |   ||||||| ||    ||||| |||||||||||||| || |||||||||||| |||||||||||||||| 
gtactttaacattcttcatagcttttattttatcttgtagtggatggtgtgtttctttgattgctcatgtgcagctagtaaaatcaaagtgagatagtggttgctatcatc-gagggcttgatttaattgctcttctcatattt---aagggtagctaatatcacctttgctttttgccctgtagGTGCTTGTAGAACCCAAAAATGCTCTTGGGAAACAGTACAAGAAACTATTTAGCATGAACAAC

upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 11
--catgtgaaatactaattttggctgtttgaagagtcatagtttttacttattttagatcttgaacagat-atatagtcatataactgttgttggttttgtagGTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTTAGCATGAACAAT
   |  |||||    ||||||   | ||   |   | |||   | ||     || |  | |  |  || | || || |    |   | |  ||  | |   |||| ||||| |||||||||||||||||||| ||||||||||||||||| |||||||||||||||
gaaacttgaaactagaattttcaatattcttaattttata--ctgtatcctcttcatttgtgaagtagcttatgtacttgctttggtttcattt-tgtaacagGTTCTCACAGAACCAAAAAATGCTCTTGGTAAGCAGTACAAGAAATTGTTTAGCATGAACAAT

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|24135727|gb|BU926237.1|BU926237
EST:     TCCCCATTTTAGTTAGCTTGTCAGCTTTAACTGAAGACCAACTTATGATG                         GTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTT
genomic: TCCCCATTTTAGTTAGCTTGTCAGCTTTAACTGAAGACCAACTTATGATGgtattcctac ... ggttttgtagGTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTT
EST: gi|16276814|gb|BI942058.1|BI942058
EST:     TCCCCATTTTAGTTAGCTTGTCAGCTTTAACTGAAGACCAACTTATGATG                         GTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTT
genomic: TCCCCATTTTAGTTAGCTTGTCAGCTTTAACTGAAGACCAACTTATGATGgtattcctac ... ggttttgtagGTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattttagatcttgaacagatatatagtcatataactgttgttggttttgtagGTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTTAGCATGAACAAT
                               atataac  putative branch site (score: 3)
                     atatatagtcatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtgaaatactaattttggctgtttgaagagtcatagtttttacttattttagatcttgaacagatatatagtcatataactgttgttggttttgtagGTCCTCACTGAACCAAAAAATGCTCTTGGCAAGCAGTACAAGAAATTATTTAGCATGAACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
catgtga
- - - - - - - - - tggctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgttg