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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttcttggtttttctacttattggtcatccttttaagatgtgtagttggagaagggagcaaggatttgttttaaacttaaaggttcaagctgattttcggaatttaaaatgtttcagGTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCACTTGCATAAATTGCTTGACAAAG

Basic information

species Glycine max
transcript GLYMA13G19230.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 18
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 18
gtatgtatttcttggtttttctacttattggtcatccttttaagatgtgtagttggagaagggagcaaggatttgttttaaacttaaaggttcaagctgattttcggaatttaaaatgtttcagGTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCACTTGCATAAATTGCTTGACAAAG
                     ||  ||      |  ||||| |       | |||    |  |        |||  |||   ||    | || || || |          ||    || ||||||||||||||||  || |||| || || ||||||||||||||| || ||||||||||||| || || |||
--------------------gtatgtacatagaactcttttcacgccctcatttgttttattg--------tttcgtttcttctagttgatttaacctaagcaatatgtctt----tgcttcagGTTATTGTCCCATTATTGGTGACGGAAGATGAGAAAACTCTTGTCGCTTGCATAAATTGTTTAACGAAG

upper sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 15
---------------------------gtatgtatttcttggtttttcta---cttattggtcatccttttaagatgtgta----------gttggagaaggg--agcaaggatttgttttaaacttaaaggttcaagctgattttcggaatttaaaatgtttcagGTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCACTTGCATAAATTGCTTGACAAAG
                            | |  | | |      |||||    ||||  |||| || |||   ||  |  |           ||| |||  |    |||| ||||   |      |||||  ||     | || |||  | ||    ||||| ||||||||| |||| ||| |||| ||||| ||||||||||||||  | |||||||||||||| |||||||||
gtacgtggctaaaattttaaactaaaattctaaaatgccaacaatttctgtgccttaagggtcttcttttggggaaataaataagccacaaattgaagagtgtttggcaatgattccctagtgtgttaaatctttt--ttaatattcttatttgctgatgttgcagGTTATTATCCCACTATTGGTGACTGAAGATGAGAAAACTCTGGTTACTTGCATAAATTGTTTGACAAAG
















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|18039838|gb|BM308132.1|BM308132
EST:     ACTGCCTCACCATTGTTTTATCTCAGAATGATCCGTTCAGATGCTTGAGT                         GTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCACTTGC
genomic: ACTGCCTCACCATTGTTTTATCTCAGAATGATCCGTTCAGATGCTTGAGTgtatgtattt ... aatgtttcagGTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCACTTGC
EST: gi|15337267|gb|BI497923.1|BI497923
EST:     ACTGCCTCACCATTGTTTTATCTCAGAATGATCCGTTCAGATGCTTGAGT                         GTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCACTTGC
genomic: ACTGCCTCACCATTGTTTTATCTCAGAATGATCCGTTCAGATGCTTGAGTgtatgtattt ... aatgtttcagGTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCACTTGC
EST: gi|18735275|gb|BM528670.1|BM528670
EST:     ACTGCCTCACCATTGTTTTATCTCAGAATGATCCGTTCAGATGCTTGAGT                         GTTATTGTCCCTCTACTGGTTACTGANGATGAGAAAACTCTTATCA
genomic: ACTGCCTCACCATTGTTTTATCTCAGAATGATCCGTTCAGATGCTTGAGTgtatgtattt ... aatgtttcagGTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttgttttaaacttaaaggttcaagctgattttcggaatttaaaatgtttcagGTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCACTTGCATAAATTGCTTGACAAAG
                         agctgat  putative branch site (score: 4)
                                      aatttaaaatgtttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatttcttggtttttctacttattggtcatccttttaagatgtgtagttggagaagggagcaaggatttgttttaaacttaaaggttcaagctgattttcggaatttaaaatgtttcagGTTATTGTCCCTCTACTGGTTACTGAGGATGAGAAAACTCTTATCACTTGCATAAATTGCTTGACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG