Sequence
atgc intronic sequence ATGC exonic sequencegtttgtctttaaagttgtctccaggtgttagggggagataatgctgttgtactaagcaaatctgattatgctggattttcagTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19170.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------------------gtttgtctttaaagttgtctccaggtgttaggggga-gataatgctgttgtactaagcaaatctgattatgctggatttt---cagTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
|| | || ||||| | | || | | | | || | || | | | || | ||||| || ||||||||||||||| || || ||||| ||||| || ||||| | | ||||||||| | |||||||| ||||| ||||| |||||||| ||||| ||
gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 3
-------------------gtttgtctttaaagttgtctccaggtgttagggggagataatgctgttgtactaagcaaatctgattatgctggatttt---cagTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
| | |||||| || | || ||||| | || || || | | | | |||| || | |||||||||||| |||| || ||||| ||||| || ||||| |||| |||||||| | |||||||| | |||||||||||||||||||||||| ||
atagttttagcactcgctgcatcattcttaaagaca----catatcttttaatttgataacatttttttaacaatcctctgttttcatgcatcatctctggcagTCATACAGCCTCTATTGCGGCTGGAAATAATGGAATTCCTGTGAGAATGCATGGCCACGAATTTGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAG
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------------------------------------gtttgtctt-taaa-gttgtctccaggtgttaggggga-gataatg-ctgttgtactaagcaaatct---gattatgctggattttca-------gTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
| |||||| |||| | | ||| || ||||| | |||| | ||| ||| || | | || || |||| |||||||||| |||| |||||||| | || || ||||| ||||||||||||| |||||||||| ||||| ||||| |||||||| ||||| ||
gttagaccatgcttccttctttattaacttcttcacttggaagtaggattcttcagatgctctctttataaggggtgctgtgctcaaaataaaagaaaactgtttctatgtcttataaacataggaaatgggtagtaccaatttgataacggttgttctgttaa-caattcccccattcttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G06740.1 (Glycine max), 3'ss of exon 3
gtttgtctttaaagttgtctccaggtgttagggggagata-------atgctgttgtactaagcaaa-----tctgattatgctggattttc-------agTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
| |||||| | | || | ||| | | ||| || || | | ||| |||| || || || || ||||||||||| |||| || || || ||||| || ||||| |||||||| |||| ||||||| || | |||||||||||||||||||||||| ||
ctgtgtcttcactcacagcatcatgc-ttaacgcaatatatcttctaatttgattattttttttaaaaatcctctgttttccatgcatcgtcatccggcagTCATACAGCCTCTATTGCGGCCGGAAATAATGGAATTCCTGTGAGGATGAATGGCCATGAATTCGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAG
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 3
------gtttgtctt-taaa-gttgtctccaggtgttaggggga-gataatg-ctgttgtactaagcaaatctgattatgct-ggattttc-------agTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
| |||||| |||| | | ||| || ||||| | |||| | ||| | | || | || | || ||| ||||||||||| |||| |||||||| | || || ||||| ||||||||||||| |||||||||| ||||| ||||| |||||||| ||||| ||
ctatttctatgtcttataaacataggaaatgggtagtaccaatttgataacgattgttcttttaacaattccccgttgttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtttgtctttaaagtt--gtctccaggt-----gttagggggagataatgctgttgtactaagcaaatct-gattatgctggattttcagTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
||| ||||| || || ||| | ||| | ||| | | | ||| | || ||||| |||||| ||||||||||| |||||||| ||||| || ||||| |||| |||||||| ||||||||||| ||||| |||||||||||||| ||||| ||
atgatagtttgattttcttttaatattttgttcccatttactctgttttatttgattgggtctggttcatttgttgtttcttgggaatactggacaa-cagTCACACAGCAGCTATTGCAGCTGGAAATAATGGAATTCCAGTGAGAATGCATGGGTATGAATTTGGGAAAGCAAGTGGGATGGCTCCCCGTGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagggggagataatgctgttgtactaagcaaatctgattatgctggattttcagTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
atctgat putative branch site (score: 4)
ttttc putative PPT
agataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtctttaaagttgtctccaggtgttagggggagataatgctgttgtactaagcaaatctgattatgctggattttcagTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC