Sequence
atgc intronic sequence ATGC exonic sequence...tagcattgacaactatgttcaataggcatcactttacaaaccaaatattaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12080.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G14170.1 (Glycine max), 3'ss of exon 3
tagcattgacaactatgttcaataggcatcactttacaaaccaaat--attaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAAC-ATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC------
||| ||| || | | | | || ||| || | |||| ||||| ||| | || || || ||| | | | | ||| | || || | | | | | | |||||||| | || |||| || ||| ||||| ||||| | |||||||||||||||||||||||||| |||||||
--------tcaaaatgaatcactaactaactcctaactaactaactgaattacaacatacatcaacagatttttcattt-tataatttactttttctgctaaactatagAAATCTAATAATCTTGTTGAAGAAGAGGATTATGTTCCGGCAATTTCAATTGTTGGTAGACCAAATGTTGGCAAAAGTAGCATTTTGAATGCACTTGTTG
upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G06150.1 (Glycine max), 3'ss of exon 6
tagcattgacaactatgttcaataggcatcactttacaaaccaaatattaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC---------
| |||||| | || | || | | | |||| ||| || | | | | | | | | | ||||| | | | || | | | | | |||||| | || |||| || ||| ||||| ||||| | || ||||||||||||||||||||||| |||||||
-------attattcttgttcactgtaca--atttggatcaacttgttttaattcatcttttgagacccttcatttttcaatttataatttactttctgctaacctatagGAATCTAATAATCTTGTTGAAGAAGATTATGTTCCAGCAATTTCAATTGTTGGTAGACCTAATGTTGGCAAAAGTAGCATTTTGAATGCACTGGTTGGTG
upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g02070.t01 (Vitis vinifera), 3'ss of exon 7
tagcattgacaactatgttcaataggcatcactttacaaaccaaatattaaaacattttcttacatctgttgcacccatacgattcaatgacttt-tctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC------
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-ttctttcatttcaatcatccataagcatgcccatattttcccctattcatctggattatatacttaggttcttgataaattttttcatgctaatatatagGATCCTGAGAATCTTGATG------GAGAAGAAAATTATGTTCCTGCAATTGCAATTGTTGGACGACCAAATGTTGGTAAAAGTAGCATTTTGAATGCATTAGTTG
upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ14023 (Selaginella moellendorffii), 3'ss of exon 4
tagcattgacaactatgttcaataggcatcactttacaaaccaaatattaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC---------
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----------------------------------------------------------gtatagatgatcagtactgaaagacaataactgtttttctatttaccagGATGAGTT--AGAAGCGAGCGAAGGCGACCGGCCTTTATCTGTGGCAATTATTGGGAGGCCAAATGTTGGCAAGAGCAGCATTTTGAATGCAATAGTCGGGAMapped 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|164010236|gb|ES134196.1|ES134196EST: GAGCTGCTTGATCTTGTTTGTTCTGGCCTAATTAAACTCGAG ATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATT
genomic: GAGCTGCTTGATCTTGTTTGTTCTGGCCTAATTAAACTCGAGgtttgtaatg ... acttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATT
EST:
gi|124739910|gb|EH831072.1|EH831072EST: GAACAGGAGAGCTGCTTGATCTTGTTTGTTCTGGCCTAATTAAACTCGAG ATCATGGAGAACATTGAAGAGGAG
genomic: GAACAGGAGAGCTGCTTGATCTTGTTTGTTCTGGCCTAATTAAACTCGAGgtttgtaatg ... acttttctagATCATGGAGAACATTGAAGAGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC
ttcttac putative branch site (score: 2)
cttttct putative PPT
aaacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagcattgacaactatgttcaataggcatcactttacaaaccaaatattaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC
- - - - acaacta
- - - - - - - - - - - - - catcact
- - - - - - - - - - - - - - - - - - caaacca
- - - - - - - - - - - - - - - - - - - - - - - attaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acccata