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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtctttgttaatatttgtcaaacatatttctccttgtatgtggaatttcccaaaatattgtaatattgcttacaattttttgtgcaaatcattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG

Basic information

species Arabidopsis thaliana
transcript AT5G50850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 3
agtctttgttaatatttgtcaaacatatttctccttgtatgtggaatttcccaaaatattgtaatattgcttacaattttttgtgcaaatcattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG-------------------
            |||   | |    | |     ||| | | |  ||| ||  || |  ||   ||      |  || |||  |      |     |  |||| || ||||| |||||||| || || ||| | |||||||||||||| |||||||||||||| ||  | ||||||||||||                   
-----------gtatgcattattgttctcatctcttatctctt-aatctcttaata-gttactatcaaatatcaaactttccgccgttgtttcgatgcagATTACTGTCAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 3
agtctttgttaatatttgtcaaacatatttctccttgtatgtggaatttcccaaaatattgtaatattgcttacaattttttgtgcaaatcattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG-------------------
                      |  ||||  |  |   || |  ||| ||   |  | ||   ||      |  || |     |     |     |  |||| || ||||| || ||||| || || ||| | |||||||||||||| |||||||||||||| ||  | ||||||||||||                   
--------------------gtatgtattattgttctcatctctaatctcttcatctcttactatcaaatatcaaactggccattgttgtttcgatgcagATTACTGTCAGGGAGGCTCTGAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 3
agtctttgttaatatttgtcaaacatatttctccttgtatgtggaatttcccaaaatattgtaatattgcttacaatttttt--gtgcaaatcattgttt------agATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG-------------------
                      |   |||  |  |   || |  ||| ||  ||  | ||    | || ||  ||| | ||   |||   ||  ||||||      |||| || ||||| || ||||| || || ||| | |||||||||||||| |||||||||||||| ||  | ||||||||||||                   
--------------------gtatgcattattgttctcatctctaatctcttaatctcttaatctcttactatcaaatattaaagtggccattgttgtttccatgcagATTACTGTCAGGGAGGCTCTGAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTG

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 3
agtctttgttaa-tatt-tgtcaaacatatttctccttgtatgtggaatttcccaaaatattgtaatattgcttacaattttttgtgcaaatcatt--gtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG
  | ||   |||  |   ||        || | ||| ||  || ||  | | || || | ||  |  | |   || | ||     |    || |||  |   |||||||||| || ||||||||||| |||||| |||||||||||||||| || ||||||||||| ||| | ||||||||||||
--ttttgactaaacaccatgctttgtggatatgtccatgcttgaggcttatgcctaactctttaagaact--ctaaatttaacaataattattattttgcacagATGACAGTGAGGGATGCTCTAAACTCTGCACTTGATGAGGAAATGTCCGCAGATCCTAAAGTCTTTTTGATGGGTGAAGAG

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|124748427|gb|EH838557.1|EH838557
EST:     CGCGATTCGCATTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAG                         ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGA
genomic: CGCGATTCGCATTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAGgtaaaatgtc ... cattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGA
EST: gi|124897590|gb|EH973804.1|EH973804
EST:     TTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAG                         ATGACAGTCAGAGATGCTCTAAATTCTGCAATCGATGAGGAAATGTC
genomic: TTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAGgtaaaatgtc ... cattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTC
EST: gi|116443796|gb|EG486388.1|EG486388
EST:     CGCGATTCGCATTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAG                         ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCT
genomic: CGCGATTCGCATTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAGgtaaaatgtc ... cattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCT
EST: gi|124946127|gb|EL022076.1|EL022076
EST:     CGCGATTCGCATTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAG                         ATGACAGTCAGAGATGCTCTAAA
genomic: CGCGATTCGCATTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAGgtaaaatgtc ... cattgtttagATGACAGTCAGAGATGCTCTAAA
EST: gi|116376958|gb|EG419550.1|EG419550
EST:     CGCGATTCGCATTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAG                         ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCT
genomic: CGCGATTCGCATTGGTTTCTGCTAGGAGCTATGCAGCTGGTGCAAAAGAGgtaaaatgtc ... cattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCT
EST: gi|124920897|gb|EH994569.1|EH994569
EST:     CTGGTGCAAAAGAG                         ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCT
genomic: CTGGTGCAAAAGAGgtaaaatgtc ... cattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCT
EST: gi|124818472|gb|EH903338.1|EH903338
EST:     CGATTCGCATTGGTTTCTTGCTAGGAGCTATGCAGCTGGTGCAAAAGAG                         ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGAT
genomic: CGATTCGCATTGGTTTC-TGCTAGGAGCTATGCAGCTGGTGCAAAAGAGgtaaaatgtc ... cattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcccaaaatattgtaatattgcttacaattttttgtgcaaatcattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG
                      tgcttac  putative branch site (score: 2)
       aaaatattgtaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtctttgttaatatttgtcaaacatatttctccttgtatgtggaatttcccaaaatattgtaatattgcttacaattttttgtgcaaatcattgtttagATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - aaacata
- - - - - - - - - - - - - -tttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - ccaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttacaa