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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttgaatcttacattattttttattctaccattgttggtgtattctgtcttcatgtactgatacttattgatgtttttgacttgtttcttgtgatgaattttaacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG

Basic information

species Glycine max
transcript GLYMA20G33910.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 12
gtctgtttgaatcttacattattttttattctaccattgttggtgtattctgtcttcatgtactgatacttattgatgtttttgacttgtttcttgtgatgaattttaacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
           || ||||  |||  ||  |    | ||  | ||| ||| | |          ||| | |  | | ||||  |   || |        || |||  |      ||||||||||| ||||||||    |||||||| |||||||||||||||||| |||||||  | || || ||||| || || |||||||| || || |||
---------gttcgtacaacattaattcattg--cgttactagtgcattattt----------tgaaaatcgtggttgttgatagattat--------ataaatgctgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTACAGGAGCGGTTGGCAAAGCTCTCCGGAGGTGTTGCTGTTCTAAAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 11
gtctgtttgaatcttacattattttttattctaccattgttggtgtattctgtcttcatgtactgata-cttattgatgtttttgacttgtttcttgtgatgaattttaacaa-acagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
                      ||  |    ||  | | ||| |||   ||||||| |  | ||  || |||  || |  |  | | || |   || ||  || | |  |     ||||||||||||||| |||| || ||||||||||||||||||||||||||| | |||||| | || || ||||| ||||| |||||||| || ||||||
---------------------gttcgtgcaatattacttttgttgtg--ctgtcttaaattgcttctaactttctggttctgataatttatggattatg--gattatggatgttgcagATTAGATCAGCAGTTGAGAACAGCACTTCAGATTATGACAAGGAAAAGCTCCAGGAACGGTTGGCAAAGCTCTCTGGAGGTGTTGCTGTTCTGAAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
gtctgtttgaatcttacattattttttattctaccattgtt-ggtgtattctgtcttcatgtactgatacttattgatgtttttgacttgtttcttgtgatgaattttaacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
    ||| |  | ||      ||||||||  |    | |||  ||||  | |  |||       |  | |  | || |  |||| |  |||||    |  |  |||  | ||  |||||  ||||     |||||   |||||||| |||||||||||||| ||||| || ||||| || || |||||||| || |||||||| ||||| |||
----gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgc-ccttttttccaactggtagttttaatatgttttgaatt-tttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 10
gtctgtttgaatcttacattattttttattctaccattgttggtgtattctgtcttcatgtactgatacttattgatgtttttgacttgtttc--ttgtgatgaattttaacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
||   ||| || |||| |   |  |  |||      ||  |  |  | | ||| | || | | | ||     |  |||    |   | |||    |||    | |||  ||| |||||||||| ||||||||||||   ||||| ||||||||||||||||||||  | || ||||| || || ||||| ||||| |||||||||||  |||||
gtaatttttaaccttataccctgataaattg----gttagtaataaaatttgtatgcaagaaattatgaa-gtgtatgaaagtagttcgttctaattgcttggtattgcaactaacagATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAG

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|24205139|gb|BU964392.1|BU964392
EST:     TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAG                         ATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
genomic: TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAGgtctgtttga ... taacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA
EST: gi|16284788|gb|BI946271.1|BI946271
EST:     CCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGGAA-GATGTGAGCAG                         AT-AGATCAGCAATTGAAA-TAGCACT-CAGATTATGA-AAGG
genomic: CCTTGATGGAGCTGGTGATAAGAAAGCAATTGA-GGAAAGATGTGAGCAGgtctgtttga ... taacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGG
EST: gi|16278620|gb|BI942998.1|BI942998
EST:     TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAG                         ATTAGATCAGCAATTGAGAATAGCACTTCAGATTATGACAAGGAAAAGTTA
genomic: TCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAGGAAAGATGTGAGCAGgtctgtttga ... taacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgatacttattgatgtttttgacttgtttcttgtgatgaattttaacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG
                                          ttttaac  putative branch site (score: 2)
                                     atgaattttaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtttgaatcttacattattttttattctaccattgttggtgtattctgtcttcatgtactgatacttattgatgtttttgacttgtttcttgtgatgaattttaacaaacagATTAGATCAGCAATTGAAAATAGCACTTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG

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