Sequence
atgc intronic sequence ATGC exonic sequencegtaaataggcttcatttgtcatttgaccctttctcttctttagctcattgccgtgacttaaaacatcattgtttatctgtagAGATGAAATAGCTGGATGCAGTGAGAAAGCATACGATCATCTCTCAATCAGTGAAGGTTGTAAGATGTTACTCTTCTCGTCTGATCAACAACTGTTAACA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42040.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G25730.1 (Glycine max), 3'ss of exon 4
-----------------gtaaataggcttcatttgtcatttgaccctttct-cttctttagctcattgccgtgacttaaaacatcattgtttatctgtagAGATGAAATAGCTGGATGCAGTGAGAAAGCATACGATCATCTCTCAATCAGTGAAGGTTGTAAGATGTTACTCTTCTCGTCTGATCAACAACTGTTAACA
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ttaaagttcaaatacctgcccctctagtggttctattattttaccatttgtgcatctatatttttttctaattagtttatatctatcttcaaacattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAAGGATGCTAAGCAAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAA
upper sequence: AT5G42040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 4
---------gtaaataggcttcattt--gtcatttgaccctttctcttctttagctcattgccgtg--acttaaaacatca-----ttgtttatctgtagAGATGAAATAGCTGGATGCAGTGAGAAAGCATACGATCATCTCTCAATCAGTGAAGGTTGTAAGATGTTACTCTTCTCGTCTGATCAACAACTGTTAACA
| | | |||||| || | | | | | | || | || | | | | ||| | ||| | | ||||| |||||||||||||| |||||||| || |||||||| |||| ||||||| ||| | | | ||||| || ||||| ||||| ||| |||| || |
attatcttctctgaaaagtatcattttaagtgctttattttgtttaatatctattttgttcctcttttaataaaagtgtttattttttggtcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAATGATGCCCGACATATGTTGCTGTTCTCTTCTGACCAAGAACTTTTTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttctcttctttagctcattgccgtgacttaaaacatcattgtttatctgtagAGATGAAATAGCTGGATGCAGTGAGAAAGCATACGATCATCTCTCAATCAGTGAAGGTTGTAAGATGTTACTCTTCTCGTCTGATCAACAACTGTTAACA
tttatct CT-rich tract
ttaaaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataggcttcatttgtcatttgaccctttctcttctttagctcattgccgtgacttaaaacatcattgtttatctgtagAGATGAAATAGCTGGATGCAGTGAGAAAGCATACGATCATCTCTCAATCAGTGAAGGTTGTAAGATGTTACTCTTCTCGTCTGATCAACAACTGTTAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG