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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaatttcttcccttgcttttgtcttctcagtctttctttatgaatttatatctttatatttactattattctaaaatcttggcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGGGGTTCTGTTAGAGCTGCAATGGGACATCCTACCCCATTTGACTTGAGAT

Basic information

species Glycine max
transcript GLYMA19G30460.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30460.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 10
-------------------------------------------------------gtaccaatttcttcccttgcttttgtcttctcagtctttcttta--tgaatttatatctttatatttactattattctaaaatcttggcatta---aaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGGGGTTCTGTTAGAGCTGCAATGGGACATCCTACCCCATTTGACTTGAGAT
                                                           |  || | |   |   | |||      |  || ||    |    ||| |   ||| |  || | | ||| ||  ||  | ||     |    | |||| |   | ||| |  ||||||||||||| ||     |   |||   ||||||||||||||||||||||||||| |||||    |  ||     |||  |
gtacgttaaatgcccaagtaagaatagtcatccaaatataactgggtagagggttactacggttccatttttccttattgcagatgccatcattgcaaaacaaaatgttgttctatgcatatgccattgtttcaagtttttttttcttattatagGATGTATTGGATAGTCTTGAATTTGCAAGGGGGAGAGCAGAATCGACATGGGGTTCTGTTAGAGCTGCAATGGGGCATCCAGAACGGTTCCCACTGAAGT

upper sequence: GLYMA19G30460.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 10
----------gtaccaa-tttcttcccttgcttttgtcttctcagtctttctttatgaatttatatctttatatttactattattctaaaatcttggcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGGGGTTCTGTTAGAGCTGCAATGGGACATCCTACCCCATTTGACTTGAGAT
           ||| || | ||||  ||||  ||     | |  ||   |  |  | |    |  | ||| | |       | |  |    |||     |  | ||||||   | ||  |  | ||||||||||| ||   | |    |||  ||||||||||||||||||||||||||| || ||    |||||     | | ||
taccaagaaaatactaaatatcttttcttgaattgaagctat--gttacttgtcgtaacaccagttttttgtttgggaacatctcttgttgtctc----tctacagGACGTATTGGACAGTCTAGAATTTGCAAGGGGGAATGCAGATTCAACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCCGAACCATTCCCTGTCAAAT

upper sequence: GLYMA19G30460.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 10
--gtaccaatttcttcccttgcttttgtcttctcagtctttctttatgaatttatatctttatatttactattattctaaaa-----tcttggca-ttaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGGGGTTCTGTTAGAGCTGCAATGGGACATCCTACCCCATTTGACTTGAGAT
   || | |        |    | |  | | || | | |     ||||    | |||| | | |   ||| || || |   |     || || |  |  | ||||||   | ||  |  | ||||||||||| ||   | |    ||   ||||||||||||||||||||||||||| || |||   |||||     | | ||
acctatccaagaaaataccaaatatcttttccttaat-tgagactatggtagt-tatcataacacc-acttttgttttgggaacgtctcctgtctctctacagGACGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCGACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAAT

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|193399461|gb|FK361351.1|FK361351
EST:     TCGGCCTTAATGATGAAATTGATACATCATCCATAGAATCCTATGTGCAA                         GACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
genomic: TCGGCCTTAATGATGAAATTGATACATCATCCATAGAATCCTATGTGCAAgtaccaattt ... gcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
EST: gi|193608896|gb|FK566072.1|FK566072
EST:     TCGGCCTTAATGATGAAATTGATACATCATCCATAGAATCCTATGTGCAA                         GACGCCCTCGATGGCATTGAATTTGTAAGAGGCTCTCCTACATCACAATGG
genomic: TCGGCCTTAATGATGAAATTGATACATCATCCATAGAATCCTATGTGCAAgtaccaattt ... gcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
EST: gi|193387375|gb|FK349600.1|FK349600
EST:     TCGGCCTTAATGATGAAATTGATACATCATCCATAGAATCCTATGTGCAA                         GACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTGCATCACAATGG
genomic: TCGGCCTTAATGATGAAATTGATACATCATCCATAGAATCCTATGTGCAAgtaccaattt ... gcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
EST: gi|208324410|gb|GE125711.1|GE125711
EST:     AATCCTATGTGCAA                         GACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
genomic: AATCCTATGTGCAAgtaccaattt ... gcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
EST: gi|193483807|gb|FK449326.1|FK449326
EST:     ATGAAATTGATACATCATCCCATAGAATCCTATGTGCAA                         GACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
genomic: ATGAAATTGATACATCAT-CCATAGAATCCTATGTGCAAgtaccaattt ... gcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
EST: gi|207842537|gb|GD815929.1|GD815929
EST:     AATTGATACATTCATCCATAGAATCCTATGTGCAA                         GACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
genomic: AATTGATACA-TCATCCATAGAATCCTATGTGCAAgtaccaattt ... gcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
EST: gi|193594010|gb|FK546252.1|FK546252
EST:     GATACATCATCCATAGAATCCTATGTGCAA                         GACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG
genomic: GATACATCATCCATAGAATCCTATGTGCAAgtaccaattt ... gcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgaatttatatctttatatttactattattctaaaatcttggcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGGGGTTCTGTTAGAGCTGCAATGGGACATCCTACCCCATTTGACTTGAGAT
                                ttctaaa  putative branch site (score: 2)
      aatttatatctttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaatttcttcccttgcttttgtcttctcagtctttctttatgaatttatatctttatatttactattattctaaaatcttggcattaaaagGACGCCCTCGATGGCATTGAATTTGCAAGAGGCTCTCCTACATCACAATGGGGTTCTGTTAGAGCTGCAATGGGACATCCTACCCCATTTGACTTGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC