Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttgatacagatttttttacctttggtttctgtcaagtgtatatgagaataattttatgtttttgtttcttagGATGCAAATCCAAGACTTTCATGCTTTGGTTTGATGAAAAACAGTAGAGATGGAAAGAGTTATAGCACTAACCTGGCATTCACTCCTCCCGAGTATCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41260.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G01730.2 (Glycine max), 3'ss of exon 5
----------------gtaagtttgatacagatttttttacctttggtttctgtcaagtgtatatgagaataatttta-tgtttttgtttcttagGATGCA-------AATCCAAGACTTTCATGCTTTGGTTTGATGAAAAACAGTAGAGATGGAAAGAGTTATAGCACTAACCTGGCATTCACTCCTCCCGAGTATCTGA
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ggcactgatactgtggaagaaactgctataaattagtgctttcttagcctaaat--agtatgtgtgactgtcctttttctttttttcctccttattattcagGAATACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGATGGGAAAAGTTACAGTACAAATTTGGCATTCACTCCACCTGAATATCTGA
upper sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 6
---------------gtaagtttgatacagatttttttacctttggtttctgtcaagtgtatatgagaataattttatgtttttgtttcttagGATGCA-------AATCCAAGACTTTCATGCTTTGGTTTGATGAAAAACAGTAGAGATGGAAAGAGTTATAGCACTAACCTGGCATTCACTCCTCCCGAGTATCTGA
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tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA
upper sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtttgatacagatttttttacctttggtttctgtcaagtgtatatgagaat----aattttatgtttttgtt---tcttagGATGCAAATCCAAGACTTTCATGCTTTGGTTTGATGAAAAACAGTAGAGATGGAAAGAGTTATAGCACTAACCTGGCATTCACTCCTCCCGAGTATCTGA
|||||| || | | |||| | |||| | | | | | | | ||||| || || | || || ||| |||||| |||| |||||||||||||||||| ||||||| || |||||||||||||| ||||||||||| ||| | || || || ||||| || |||||||
gtaagtatgttgctttttttcaattttatggtattttttttttctcttttagaatctttgatacattgctcttattaaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGATGGAAAAAGTTATAGCACAAACTTAGCCTTTACACCTCCTGAATATCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctttggtttctgtcaagtgtatatgagaataattttatgtttttgtttcttagGATGCAAATCCAAGACTTTCATGCTTTGGTTTGATGAAAAACAGTAGAGATGGAAAGAGTTATAGCACTAACCTGGCATTCACTCCTCCCGAGTATCTGA
tgtttttgtttctt CT-rich tract
tatatgagaataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttgatacagatttttttacctttggtttctgtcaagtgtatatgagaataattttatgtttttgtttcttagGATGCAAATCCAAGACTTTCATGCTTTGGTTTGATGAAAAACAGTAGAGATGGAAAGAGTTATAGCACTAACCTGGCATTCACTCCTCCCGAGTATCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC