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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttctagaagcgcagaatgctgaatttattttcttttgattcactgcactagttttttaagactccggaatctctgttgttaatatttctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT

Basic information

species Glycine max
transcript GLYMA04G00200.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G00200.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g58590.1 (Oryza sativa), 3'ss of exon 11
gtatgtgttctagaagcgcagaatgctgaatttattttcttttgattca-ctgcactagttttttaagactccggaatctctgttgttaatatttctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT
||||||  | ||  |      |||  |   |  |    |      |||| ||||| | || | | |   ||  |       |  ||| | | |   ||||  ||  | || ||||| ||||| || ||||||||||||||||||||||| |||||  | || ||| 
gtatgttgtatattatatattaattatagttggaaagccaaggatttcatctgcaat-gtatctaattgctttgctgctattcctgtcactgtgg-tattgaagGACAATCATGGCCGTTTCTTCCTGGAATGACAATGGACAAAAGCAATTTGTTTACGACCCAA

upper sequence: GLYMA04G00200.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G426275_T04 (Zea mays), 3'ss of exon 11
gtatgtgttctagaagcgcagaatgctgaatttattttcttttgattcactgcactagttttttaagactccggaatctctgttgttaatatttctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT
   | |||| |   |    |   ||||   |  ||     | |||      | ||| | | | |||   |||    | | |  |  | ||  || ||    ||  | |||||||||||||| || |||||||||||||| || |||||||||||  | || ||| 
--gtatgttatgttattata---tgctttctacatacaaatatgag-----gaacttgatatataaatttcct---tttattctaatcattgttgtacggaagGACGATTATGGCTGTTTCTTCTTGGAATGACAATGGGCAGAAGCAGTTTGTTAACGACCCAA

upper sequence: GLYMA04G00200.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G38240.3 (Arabidopsis thaliana), 3'ss of exon 11
gtatgtgttctagaagcgcagaatgctgaatttat---tttcttttgattcactgcactagttttttaagactccggaatctctgttgttaatatttctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT
||||||   |||     ||   |  || |   |||   ||||    || |      |    ||| |||    | |  | ||| |  || |   |    | |  |||| |||||||||||| ||| ||||||||||| |||||||| ||||||||||| |||||||| |
gtatgttacctactgaagctagactcttatagtataagtttccacagagtatacaaatgtttttattactgtttctcattcttttctggtc-caaacatgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGTGCATGATCCCT

upper sequence: GLYMA04G00200.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0972g00010.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtgttctaga--------agcgcaga-atgctgaattt-attttc------ttttgattcactgcactagttttttaagactccggaatctctgttgttaatatttctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT--------------
|| ||| || | ||        ||| || | | | | ||||| |||||       | || ||| ||| ||    | |  |     | | | |  |   ||| || ||   | ||  ||| ||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||||| |              
gtgtgtcttttggatgaactaaagctcatataagttaaatttcatttttagaagttattaattaacttcagagttctgatgttttttctgcacttaccttggta-taaaaccatgatagGTCCATTATGGCTGTTTCTTCATGGAATGACAATGGGCAAAAGCAGTTTGTGCATGATCCTTGTAAGCTCTTCTGA

upper sequence: GLYMA04G00200.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0585g00030.t01 (Vitis vinifera), 3'ss of exon 11
gtatgtgttctagaagcgcagaatgctgaatttattttcttttgattcactg----cactagtt--ttttaagactccggaatctctgttgttaatatttc----------tattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT
|| ||| |||| || |  |  || ||| |  | | ||   ||| |||    |     | || ||   || |    || |   | | |  ||    ||  ||           ||  ||| ||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||||| |
gtgtgtcttctggatgaactaaa-gctcatataagttaaatttcatttttagaagttattaattaacttcagagttctgatgttttttctgcacttacctcggtataaaaccatgatagGTCCATTATGGCTGTTTCTTCATGGAATGACAATGGGCAAAAGCAGTTTGTGCATGATCCTT

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|10842801|gb|BF066219.1|BF066219
EST:     GATTTCTTTGATTATTTTGAAGCTGCAGCGAGTCTCCTTGAGAAGGATAA                         ATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGT
genomic: GATTTCTTTGATTATTTTGAAGCTGCAGCGAGTCTCCTTGAGAAGGATAAgtatgtgttc ... tctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGT
EST: gi|192297484|gb|FG989519.1|FG989519
EST:     GATTTCTTTGATTATTTTGAAGCTGCAGCGAGTCTCCTTGAGAAG-ATAA                         ATCCATTATGGCTGTTTCCTCATGGAATGACA-TGGACAAAAGCAGTTTGT
genomic: GATTTCTTTGATTATTTTGAAGCTGCAGCGAGTCTCCTTGAGAAGGATAAgtatgtgttc ... tctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGT
EST: gi|14011124|gb|BG726055.1|BG726055
EST:     GATTTCTTTGATTATTTTGAAGCTGCAGCGAGTCTCCTTGAGAAGGATAA                         ATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGT
genomic: GATTTCTTTGATTATTTTGAAGCTGCAGCGAGTCTCCTTGAGAAGGATAAgtatgtgttc ... tctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgcactagttttttaagactccggaatctctgttgttaatatttctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT
                                   tgttaat  putative branch site (score: 3)
                                           tttctattct  CT-rich tract
                                  ttgttaatatttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgttctagaagcgcagaatgctgaatttattttcttttgattcactgcactagttttttaagactccggaatctctgttgttaatatttctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA