Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtaccgtacatgcctttatgtttagatcgggggatagtaggtgtcaatcaactatgctattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA

Basic information

species Glycine max
transcript GLYMA19G43800.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 3'ss of exon 2
tttgtaccgtacatgcctttatgtttagatcgggggatagtaggtgtcaatcaactatgctattgaaaataatttat---tttttttggccttctttta--ccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA
             ||||   ||| | | |       |    |  | |  ||      | | |    || | ||||||   || || | ||||| ||  |   |||||||| |||||||| || |||||||||||||| || ||||||||||||||||| || || |||||||| ||||| |||||||| ||||||||||| ||||
------------gtgcccc-atgctcacaatt----acctgacctttttatttttcttaccaagtgaattgatttatcagttattcttgccttgttggaattcagGTTGTCGAAGATGGGTACGAGTTCTTTGCTAACCGCCAACTTGTAACAATATTCTCGGCCCCTAATTACTGTGGAGAATTTGATAATGCTGGTGCCATGA

upper sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G112240_T01 (Zea mays), 3'ss of exon 2
tttgtaccgtacatgcctttatgtttagatcgggggatagtaggtgtca-atcaactatgctat-tgaaaataatttattttt--tttggccttctttta--ccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA
             ||   |  | || |    | |   || |   |  |  || |||||     | |   |||| |||| || |  ||| || || ||  |   |||||||| ||||||||||| ||||| || ||||  || ||||| ||||||||||||||||| ||||| || ||||| ||||| ||||| |||||||| ||||
-----------gttgttgtgttcttaaagatgtgacctacttattaccttataaactacaaagtgtatcaatagtttacttatgcttttgcattgttgaaattcagGTTGTCGAAGATGGATACGAGTTTTTCGCTAGCCGTCAACTCGTAACAATATTTTCAGCCCCTAACTACTGTGGAGAATTCGACAACGCTGGTGCCATGA

upper sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
tttgtaccgtacatgcctttatgtttagatcgggggatag-taggtgtcaatcaactatgc-tattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA
              |    | || |  ||  | | |  |  ||  | |      |  | |  |||  |   |    |  | |||||| |||  |     |||||||| ||||||||||||||||| || ||||  || ||||| |||||||| |||||||| ||||| || ||||| |||||||| || |||||||| ||||
--------------gttgctgtgctctgaaagagtgtgacctacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA

upper sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
tttgtaccgtacatgcctttatgtttagatcgggggatagtaggtgtcaatca-----actatgctattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA
     |    |  || || ||      |   || |  || ||  | | | |||     |||    | || | |    ||| | |    |    ||  ||| | ||||||| || ||||| ||||| |||||||| || || ||||||||||| |||||||| || ||||||||||||||||| ||||| ||||||||||| ||||
----cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaattttcatagaggtttttctaagataaaattaatttgc-agGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA

upper sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
tttgtaccgtacatgcctttatgtt-tagatcgggggat--agtaggtgtcaatcaactatgctattgaaaataatttattttttttggccttcttttac-cagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA
  || |||     |   || ||| | | | | |     |  ||  | |||   | |  |    | |  | |||   | || | |   ||   ||   | | ||||||||||| ||||| || ||||| || ||||| || ||||| || || || || || ||||| ||||||||||| |||||||| ||||| ||||| ||||
--tg-accagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatg-ctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

upper sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ20637 (Selaginella moellendorffii), 3'ss of exon 2
tttgtaccgtacatgcctttatgtttagatcgggggatagtaggtgtcaatcaactatgctattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA
                             |  |  | | ||  || ||  ||      | |  |   |      | | |    |  |       || ||||| |||||||| ||||| ||||| || || ||  |||||||||| || |||||||| ||||| || ||||||||||| || |||||| | || |||||||
----------------------------gtatgatgctcgtgagt-tctttctttctcgttgctttgagccccatgtctgcaataaca-----ataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA

upper sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
tttgtaccgtacatgcctttatgtttagatcgggggatagtaggtgtcaatcaactatgctattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA
                             |  |  | | ||  || ||  ||     || |  |   |      | | |    |  |       || ||||| |||||||| ||||| ||||| || || ||  |||||||||| || |||||||| ||||| || ||||||||||| || |||||| | || |||||||
----------------------------gtatgatgctcgtgagt-tctttctttattgttgctttgagccccatgtctgcaataaca-----ataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA

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|6133946|gb|AW132339.1|AW132339
EST:     CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAG                         GTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... cttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
EST: gi|8669886|gb|BE190993.1|BE190993
EST:     CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAG                         GTTGTGGAAGATGGATATGAGTACTTTGCTAATCGACAACTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... cttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
EST: gi|208067226|gb|GD862234.1|GD862234
EST:     CTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAG                         GTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
genomic: CTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... cttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
EST: gi|298189387|gb|HO037790.1|HO037790
EST:     CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAG                         GTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... cttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
EST: gi|192299585|gb|FG993255.1|FG993255
EST:     CAGAGTTTTTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAG                         GTTGTGGAAGATGGATATGAGTTCTTTGTTAATCGACAACTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... cttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
EST: gi|298189504|gb|HO037907.1|HO037907
EST:     CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAG                         GTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... cttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
EST: gi|151403035|gb|EV272848.1|EV272848
EST:     CAGAGTTTCTTCGGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAG                         GTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... cttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
EST: gi|6482298|gb|AW201567.1|AW201567
EST:     CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAG                         GTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... cttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
EST: gi|298167241|gb|HO010680.1|HO010680
EST:     CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAG                         GTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA
genomic: CAGAGTTTCTTCAGAAACATGATCTTGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... cttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaatcaactatgctattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA
                           tttattttttttggcc  CT-rich tract
     tcaactatgctattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtaccgtacatgcctttatgtttagatcgggggatagtaggtgtcaatcaactatgctattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - -catgcct
- - - - - - - - - - - - - - - -gggggat
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa