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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtgtgattattatattggtgatttgaatttaaataattcgttgggagccatgatatcgtttccttacaaatcgcagGAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAATTTGTCCGACTCCAGACTTTTAACCGAAGTGGATTCCAGCAAATTCAAT

Basic information

species Glycine max
transcript GLYMA02G01610.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01610.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os03g52770.1 (Oryza sativa), 3'ss of exon 18
-------------------gtattgtgtgattattatattggtgatttgaatttaaataattcgttgggagccatgatatcgtttccttacaaatcgcagGAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAATTTGTCCGACTCCAGACTTTTAACCGAAGTGGATTCCAGCAAATTCAAT
                    |   ||   ||| |  | |   |    | |  ||||    ||   |    |  ||  |     ||       |||  ||||| |||||  || |  || |  | ||  |  |||| ||||| || ||||||||||| || || ||||| || ||| |||||||||| |||||||||||  
ctggttgacttgcttggtgatcaagttaaattttcttgtctatagcatcatcttaatctgtttcctaaatgtaattcttcatattatgggtgaatttcagGAATCTGTAATTTCTGCTGTCCTCAAGCTCTGCCTGAAAAGCTTGCAAGAATTTGTTCGGCTTCAGACATTCAACAGAAGTGGATTTCAGCAAATTCAGC

upper sequence: GLYMA02G01610.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G023858_T01 (Zea mays), 3'ss of exon 18
----------------gtattgtgtgattattatattggtgatttgaatttaaataattcgttgggagccatgatatcgtttcctt---acaaatcgcagGAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAATTTGTCCGACTCCAGACTTTTAACCGAAGTGGATTCCAGCAAATTCAAT
                 || | |   ||| || |       |   |||  | | |    |  |     |  | ||  | | |  ||     ||||  ||||| |||||| || | ||| |  | ||  |  |||| ||||| || |||||||||||||| || |||||||| ||| |||||||||| ||||| |||||  
tttgggcagatacgctatagttttacatttttcttccatctacaggaacatcacttggccacttttgactgtaattccttgtattttgggtaaatttcagGAATCTGTTATTTCTACTGTCCTCAAGCTCTGCCTGAAAAGCTTGCAAGAATTTGTCCGTCTTCAGACTTTCAACAGAAGTGGATTTCAGCAGATTCAGC

upper sequence: GLYMA02G01610.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 18
gtattgtgtgattatta-tattggtgatttgaatttaaataatt--cgttggga-gccatgatatcgtttccttacaaatcgcagGAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAATTTGTCCGACTCCAGACTTTTAACCGAAGTGGATTCCAGCAAATTCAAT
     || |||||| |  |  ||    ||| |||       |||   ||||| | |  ||||    || | |||  |||| ||||||||| ||||| |||||| | || ||  |  | || || ||||| || ||||||||| |||| || ||||||||||| |||||||| ||||||||||| |
-----gtatgattactggtggtgccattttaaataattggtattggtgttggaatgaaatgaaggagtgtgcttgtaaattgcagGAGTCAGTTGTAACAACTGTCGTAAAGCTTTGTCTCAAGAGTTTGCATGAATTTGTCAGACTTCAAACTTTTAACCGGAGTGGATTGCAGCAAATTCAGT

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|193583229|gb|FK539731.1|FK539731
EST:     AATTGTTTAAGCAGAAAGTTGAAATTTTCACAAAAGTAGAATATACACAG                         GAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAA
genomic: AATTGTTTAAGCAGAAAGTTGAAATTTTCACAAAAGTAGAATATACACAGgtattgtgtg ... caaatcgcagGAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAA
EST: gi|10710601|gb|BF010319.1|BF010319
EST:     AATTGTTTAAGCAGAAAGTTGAAATTTTCACAAAAGTAGAATATACACAG                         GAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAA
genomic: AATTGTTTAAGCAGAAAGTTGAAATTTTCACAAAAGTAGAATATACACAGgtattgtgtg ... caaatcgcagGAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaatttaaataattcgttgggagccatgatatcgtttccttacaaatcgcagGAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAATTTGTCCGACTCCAGACTTTTAACCGAAGTGGATTCCAGCAAATTCAAT
                                       tccttac  putative branch site (score: 2)
                                     tttccttac  CT-rich tract
     atttaaataattcgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtgtgattattatattggtgatttgaatttaaataattcgttgggagccatgatatcgtttccttacaaatcgcagGAGTCTGTTGTTACAACTATAGTTAAATTGGGCCTTAAAAGTTTACAAGAATTTGTCCGACTCCAGACTTTTAACCGAAGTGGATTCCAGCAAATTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA