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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattgtttataaaatgtcatcttctctaaactaatgggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA

Basic information

species Glycine max
transcript GLYMA06G46940.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 18
--------------gtaagattgtttataa-aatgtcatcttctctaaactaat----gggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
               ||   || | |||     | |     | | ||  ||  |    |  ||||  |     |  ||    || | |   | || ||||||  ||||  | |||||||| |||||||||||||| || |||||||| || ||||| || ||||| || || || || ||||| || ||  |||| ||| 
aaattatgttgccaatacctttttctatcttggttttgcgctttatattcttgtacctgcaaattgacaagaaaatatatcttcttatgcttgttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGACAAAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATG

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 18
-----------------gtaagattgtttataaaatgtcatcttctctaaactaatgggaattttctttttataatcatctcatttatatcttc--tcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
                  |   ||| ||||  |   |    ||  | |||  |  |        |      |||||    |   ||||   |||  ||||||| | ||| | |||||||| || ||||||||||| ||||||||||| || || |||||||||||||| || || || ||||| || ||  |||| ||| 
tttaatccagtgatgcctttgtattttttaatactggcgcactgttttaacttgctactgtacattaacaaataatgcatttggttatgctttctatcagGGAGGCGATCTGACAGAGATTGGTGAAAGAGGAGTTAATATTAGTGGAGGGCAGAAGCAAAGAGTTTCAATGGCAAGAGCTGTGTATTCTGATTCAGATG

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 20
lower sequence: AT1G30410.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaagattgtttataaaatgtcatcttctctaaactaatgggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
|| |  | |   || ||| ||   |    || |   | ||  |   || || |||  | | ||     | |   |  |||||| |||||| |||| ||||| |||||| | || || |||||||| || || || ||||| ||||| || || |||||||| || ||||||||||| ||| 
gttaagtgg--aatgaaaggtttacacaactcagtaattgatatgatttttcttactaacttcctgaatttgcttattcagGGCCGTGATCTTACTGAGATTGGAGAACGTGGGGTGAATATTAGCGGAGGGCAGAAGCAGAGAGTCTCAATGGCTAGGGCAGTCTACTCAAATTCAGATG

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 20
lower sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 18
gtaagattgttta-taaaatgtcat-cttctctaaactaatgggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
        ||| | ||||||| ||  | |    || |   |        | | ||  |||    || | || |   |  |||||| ||||||  ||| ||||| |||||| | || || ||||||||||| || || ||||| |||||||| || |||||||| || ||||||||||| ||||
--------gttaagtaaaatgacaggcatacacaacccggtacatgacatttcttactaacttcctgaatt-tgcttattcagGGCCGTGATCGTACTGAGATTGGAGAACGTGGGGTGAATATTAGTGGAGGGCAGAAGCAGAGAGTTTCAATGGCTAGGGCAGTCTACTCAAATTCAGATA

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv10s0003g04450.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------gtaagattgtttataaaatgtcatcttctctaaactaatgggaatttt-ctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
                               || | ||| |   ||  |||| || |||  |    | || ||  |||| | |  | |  |  |      | | | |||||| || | |||| ||||||| || || |||||||| || |||||||||||||| ||||||||||||||||||                               
gttaagtgtattcacaaaattatacattccagtta-attctcattaggatgtaattttcattgtgttgataggttttttacctaatgtcttatttatcccttttttttctcaagGTCATGATCTTACAGAAATTGGTGAAAGAGGGGTGAATATTAGTGGTGGGCAAAAGCAAAGAGTTTCC-------------------------------

upper sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 3'ss of exon 19
gtaagattgtttataaaatgtcatcttctctaaactaatgggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
|| ||  | || | |||  || || |  | | |  |  |    |||  || |||  | | ||||   ||     || |||||| | |||| ||||||||||||| ||||| || || ||||| || ||||| ||||||||||||||||| || |||||||||||||| || ||||| ||| 
gtgagtgtattcacaaa--gttatgtcgtttcattttgttttgattgcctgttttgatttatctttctt-----ttttcagGGTCATGATCTTACAGAGATCGGTGAAAGGGGGGTGAATATCAGCGGTGGGCAAAAGCAAAGAGTTTCAATGGCTAGGGCTGTATATTCTAATTCAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctaaactaatgggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
      aactaat  putative branch site (score: 2)
                                            tatcttctc  putative PPT
                aattttctttttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattgtttataaaatgtcatcttctctaaactaatgggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG