Sequence
atgc intronic sequence ATGC exonic sequencegtgcttttcacctttaatattgttagccagatgattcaataaatagacctagcaaggtgcctaattctgactttttcatttgcctgctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31750.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 4
----gtgcttttc-acctttaatattg------------ttagccagatgattc---aataaatagacctagcaaggtgcctaattctgactttttcatttgcctgctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA
| ||| | ||| | |||| | |||||| |||| | | | ||| | | | | ||| || | | | ||| | || | ||||||||||||| ||||| || ||||| || ||||| ||||| ||||||| ||| |||||||||||||| ||||| || || || ||||| | ||||||||
gtgcataatttcctgcctatgatatagcatcatgatcccttagcctgatgttctccaacttgataaattctg-agaataactattttttcccctcctgccaaactgtttttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATCAAAACAGAGATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGA
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G12220.2 (Glycine max), 3'ss of exon 3
----gtg-cttttcacctttaatattg------------ttagccagatgattc---aataaatagacctagcaaggtgcctaattctgactttttcatttgcctgctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA
|| || | |||| | | || | |||||| |||| | | | ||| | | | | | ||| || | | | ||| | || | ||||||||||||| ||||| || ||||| || ||||| ||||| ||||||| ||| |||||||||||||| ||||| || || || ||||| | ||||| ||
gtgtgtaatttcttacctatgacatagcaccatgatcccttagcctgatgttctccaacttgataaatcccg-agaataactattttttcccctcctgccaaactgtttttctccacagCTGATGCATATAACCATACCGACTCTGAATTTCTGAAATCTGAAAATAATCAAAACAGAGATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGCGA
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 4
-----gtgcttttcacctttaatattgttagccagatgattcaataaatagacctagcaaggtgcctaattctgactttttcatttgcctg---ctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA
|| | |||| | | | | || ||| | | | | || | | || || | ||||||| | || | || | |||||||||||||||| || || ||| | ||||| || |||||||||||||| || ||||||||||| || ||||| || || || || || |||||||||||
gtatgttgactcctacctgtcacttccagatccttatgtctgatgttctccgatttgctaaat-ccaaagaataactttttttcctaccaaaattttctttccacagCTGATGCATACAATCATACTGACACTGAGTTGCTGAAATCAGAAAATAGCCATAACAGAGATGCAGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGA
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 3
-----gtgcttttcacctttaatattgttagccagatgattcaataaatagacctagcaaggtgcctaattctgactttttcatttgcc---tgctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA
|| | |||| | | | || || | | | | | || | | || || | ||||||| |||| | | || | ||||||||||||| || || || || || ||||| || |||||||||||||| || || ||||||||||| ||||| || || || || || |||||||||||
gtatgttgtctcctacctgtcagttccaggtccttatatctgatgttctccaatttgctaaat-ccaaagaataactttttt-cctgccaaatttttctttccacagCTGATGCATATAATCATACCGATTCTGAGTTGCTGAAATCAGAAAATAGCCATAATAGAGATGCTGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGA
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 4
gtgcttttcacctttaatattgttagccagatgattcaataaatagacctagcaaggtgccta------attctgactttttcatttgcctgctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA
||| | | || || | | | | | |||| | | ||| | || || | || | || | || ||| |||||||||||||||| || ||||||||||| ||||| ||||||||||||| |||||| ||||||||||| ||||| || || || || ||| | ||||||||
----gtttgtttcctgactgtgccagtaatgtcactt--tctatagcctgtatgaagtgttcactctaaatactactgtcttaaattatcctctgtacatg-cagCTGATGCATACAAGCACACAGACTCAGAATTTCTGAAATCAGAAAATAATCAGAATAGAGATGCTGGATCAACTGCCTCCACCGCTATCCTTGTTGGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agacctagcaaggtgcctaattctgactttttcatttgcctgctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA
ttctgac putative branch site (score: 2)
ctttttcatttgcctg CT-rich tract
tttttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttttcacctttaatattgttagccagatgattcaataaatagacctagcaaggtgcctaattctgactttttcatttgcctgctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG