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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaagtgtctatatggtattgacctggcttgttagttttggcctgcaaatgagtctacatattgtttctctatgtttataaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA

Basic information

species Glycine max
transcript GLYMA11G01380.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
attaagtgtctatatggtattgacctggcttgttagttttgg-cctgcaaatgagtctacatattgtttctctatgtttataaatttatattgc--cttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA
   |  |||   ||  |  || |   || ||  ||    |     |   | |  | || || |||     | | || | |||  | | |  |||  ||   |||||||||||| ||||||||||| || || ||||| || || || |||||||||||||| || ||||| ||  | |||||  | ||||||||||| || ||
ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtttcactttgcctgcaaatt---catgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 2
----------------------------------------------attaagtgtctata-tggtattgacctggcttgttagttttggcctgcaaatgagtctacatattgtttctcta-tgtttataaat-ttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA
                                               | ||   |   || |   | |   |   ||    |    || | ||||| ||| ||  |   |  | | | || ||     |     | |||  | ||| |||||||||||| ||||| ||||| || || |||||  | ||||| || ||||||||||| || || ||||| || ||||| || ||||||||||| || ||
gtccgattgtaccacctatctgcttgtgcatttcataacttttggtttcaaccattgctaattacagttgtccaactctgca--cctgccatgcaattgattcgtccgttcatatgtttagtgacagcatgcactttatcacattgtagGTTTCAATGTTGAGAAGGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAA

upper sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
attaagtgtctatatggtattgacctggcttgttagttttggcctgcaaatgagtctacatattgtttctc-tatgtttataaatttatattgcct-tgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA
          ||  |   ||||  |  || | ||  ||||    |||   |     |  || ||    |   | |  | |  | |||| ||| | |   ||||||||||||| |||||||||||||| || ||||| || |||||||||||||||||||| || |||||||| || |||||  | |||||||| || || ||
---------gtaggtcagattgctcaagcatttttattttt-tttgcgttttctcatttatcttacaacgggtttactgaggattttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA

upper sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
attaagtgtctatatggtattgacctggcttgttagttt--tggcctgcaaatgagtctacatattgtttct-ctatgtttataaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA
 |   ||| |  |||  | ||  |   | || ||  | |       | |   ||  | |    ||| | ||| ||     | |||| |||| || |    |||| |||||||| |||||||||||||| || ||||| || |||||||||||||||||||| || ||||||||||| || || ||||||||||| || || ||
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttact---cagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA

upper sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 2
-attaagtgtctatatggtat-tgacctggcttgttagttttggcctg-caaatgagtctacatattgtttctctatgtttataaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA
 |  |  ||   |||| |||  ||   |    | |   | |||   || | ||||   || || |||| || |     || || | ||| |  |    |  |||||||||||||||||||||||||||||| || || || |||||||| |||||||| || |||||||||||||| |||||||| |||||||| || |||||
taacagttgatcatattgtacatgtattatactatggatgttgatgtgtcgaatggagcttcagattgatttta---attgatcattttctggtaatatatagGTTTCAATGTGGAGAAAGTTCAGTATAAGAACGTGATGTTCACAGTGTGGGATGTAGGTGGACAAGAGAAACTCAGGCCACTCTGGAGGCATTACTTTAA

upper sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------attaagtgtctatatggtattgacctggcttgttagttttggcctgcaaatgagtctacatattgtttctctatgtttataaatt-tatattgc------cttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA
                                                                            | |     | ||||   | |||  |   | | ||   |      ||||  ||||| |   |   | |    | ||||  ||||||  || || |       || |||| |||||||| ||||||||||| || || ||||||   || ||||| ||||| |||||||| ||||||||| |  | || || ||| |||| || || ||
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttg--caaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA

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|5057972|gb|AI736448.1|AI736448
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298199192|gb|HO042555.1|HO042555
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298170232|gb|HO018856.1|HO018856
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298188565|gb|HO035258.1|HO035258
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298172316|gb|HO019356.1|HO019356
EST:     GAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: GAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298185092|gb|HO030305.1|HO030305
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|192296463|gb|FG989828.1|FG989828
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaatgagtctacatattgtttctctatgtttataaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA
                                            ttgcctt  CT-rich tract
           tacatattgtttctct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaagtgtctatatggtattgacctggcttgttagttttggcctgcaaatgagtctacatattgtttctctatgtttataaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG