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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttgaatcttccactattattaatttttattctaccattgttggtgtattctgtttcatgtactgatacttattgatgttttttacttgtttcttgtgatgaattttaacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG

Basic information

species Glycine max
transcript GLYMA10G33680.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 12
gtctgtttgaatcttccactattattaatttttattctaccattgttggtgtattctgtttcatgtactgatacttattgatgttttttacttgtttcttgtgatgaattttaacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
                                  |||   ||   ||  |  |||  ||| |  || |      ||    ||  |  ||  |  |   || | || |||  |     |||||||||||| ||||||||    |||||||| |||||||||||||||||| |||||||  | || || ||||| || || |||||||| || || |||
---------------------------------gttcgtacaacattaattcattgcgttactagtgcattattttgaaaatcgtggttgttgatagattat-ataaatgctgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTACAGGAGCGGTTGGCAAAGCTCTCCGGAGGTGTTGCTGTTCTAAAG

upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 11
gtctgtttgaatcttccactattattaatttttattctaccattgttggtgtattctgtttcatgtactgatacttattgatgttttttacttgtttcttgtgatgaattttaacaa-gcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
                            ||  |    ||  | | ||| |||  | | ||  ||    |   ||||  || |  |  | | || |   || ||  || | |  |    |||||||||||||||| |||| || ||||||||||||||||||||||||||| | |||||| | || || ||||| ||||| |||||||| || ||||||
---------------------------gttcgtgcaatattacttttgttgtgctgtcttaaattgcttctaactttctggttctgataatttatggattatg--gattatggatgttgcagATTAGATCAGCAGTTGAGAACAGCACTTCAGATTATGACAAGGAAAAGCTCCAGGAACGGTTGGCAAAGCTCTCTGGAGGTGTTGCTGTTCTGAAG

upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
gtctgtttgaatcttccactattattaatttttattctaccattgttggtgtattctgtttcatgta-ctgatacttattgatgttttttacttgtttcttgtgatgaattttaacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
||  |  ||  | |  |  | |||| | ||  |  |  |   |  |     | | |  |||  |  | ||| || || || || | ||||   | |||          |||  | || ||||||  ||||     |||||   |||||||| |||||||||||||| ||||| || ||||| || || |||||||| || |||||||| ||||| |||
gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagtt-ttaatatgttttgaattttt----------attaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG

upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 10
gtctgtttgaatcttccactattattaatttttattctaccattgttggtgtattctgtttcatgtactgatacttattgatgttttttacttgtttcttgtgatgaattttaacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
||   ||| || |||  ||  | || ||||  | |  ||  |   || || |        | ||| | ||     |     |  ||  | ||  || ||||    | |||  ||| | |||||||| ||||||||||||   ||||| ||||||||||||||||||||  | || ||||| || || ||||| ||||| |||||||||||  |||||
gtaatttttaaccttataccctgataaattggt-tagtaataaaatttgtatgcaagaaattatgaagtg---tatgaaagtagttcgttctaattgcttg----gtattgcaactaacagATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAG

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|120495061|gb|EH223228.1|EH223228
EST:     TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAG                         ATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
genomic: TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAGgtctgtttga ... taacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
EST: gi|16284045|gb|BI945876.1|BI945876
EST:     TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAG                         ATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
genomic: TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAGgtctgtttga ... taacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
EST: gi|193723968|gb|FK656332.1|FK656332
EST:     GAAAGCAATTGAAGAAAGAAGTGAGCAG                         ATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGAC-AGGAAAAGTTA
genomic: GAAAGCAATTGAAGAAAGAAGTGAGCAGgtctgtttga ... taacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
EST: gi|17400780|gb|BM177562.1|BM177562
EST:     TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAG                         ATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
genomic: TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAGgtctgtttga ... taacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
EST: gi|15813269|gb|BI785544.1|BI785544
EST:     TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAG                         ATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
genomic: TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAGgtctgtttga ... taacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
EST: gi|16278473|gb|BI942922.1|BI942922
EST:     TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAG                         ATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
genomic: TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAGgtctgtttga ... taacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgatacttattgatgttttttacttgtttcttgtgatgaattttaacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
                                          ttttaac  putative branch site (score: 2)
        ttattgatgtttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtttgaatcttccactattattaatttttattctaccattgttggtgtattctgtttcatgtactgatacttattgatgttttttacttgtttcttgtgatgaattttaacaagcagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG