Sequence
atgc intronic sequence ATGC exonic sequence...aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttcttatgcttgcaatgaaactttaactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G17150.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 6
aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttcttatgcttgca--atgaaactttaactcctttttcaatt----agGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
| | ||| ||| | || | ||| | | | || | | ||| | || || |||||| || || || || | ||| ||| ||||||| ||||||||||||||||||| ||| ||||||| | || || |||||| |||| |||||||| || |||| ||
-tagtttcatgttaattgtctgctaagtta-agtgcctaactgcccact---gac-tgttgcaatacttgcatcatataatgtttgctattatttatattgttcagGTTAAGATGGCTGTGCAGTACATGCGCCGTGTAATTCAAAGAAGAGCTAAGTTTGATATAATGGATCTTGATGTTGTTCAG
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 6
aagggtccatattagtctccttatc--cattacaatcaatggtagcgt----attctagacattttcttatgcttgcaatgaa--actttaactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG-
||| ||| ||||| || | | || ||| | | | | | | | | || || | || | | | | || | | ||||||| ||||||| |||||||||||||| || |||||||||| || |||||| | || |||||||| ||| || |||||
------tcatctta-catccttgctagcacaagagtctatgaaatcctcgagaccattgctgtaattgtaaagttttattgggttgttctgaattctgtcctt-tcagGTTAAGATGGCTGTACAGTACATGCGGCGAATCATTCAGAAAAGAGCTAAGTTTGACATAATGGATCTAAAT-GTTTTAAGG
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 7
aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttcttatgcttgcaatgaaactttaactcc--------tttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
||| | | | | | || | || | || | | || | || |||||| || | | | | ||| | || | |||||||||||||| ||||||| |||||||||||||| | ||| |||| ||||| |||||| |||||||| |||| || ||| | ||
--aaatcctt--caagcaacatggaaataa-aacctatagctgt-taacttgga--ttttctggtgtgtttattaagtcttgtattctgctggatttgcctcaattagGTTAAAATGGCTGTACAGTACATGCGGCGGGTTATTGAGAAGAAGGCAAAGTTTGATATTATGAATCTGAACTGTTTGCAG
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 7
-aagggtccatattagtctccttatccattacaatc-aatggtagcgtattctagacattttcttatgcttgcaatgaaactttaactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
| | | | |||| || | | | | | | | || | | | | || || || || | | | ||||||||||||| ||||||| || ||||||||||| | ||| |||| |||||||||||| |||| ||||| || || ||| | |
atggcagttaaacttgtcttctagactgtaatattttggacattactagttttggttaagtctgactgtctgagattttgct--gatctggtctacaattagGTTAAAATGGCTGTACAATACATGCGGCGGGTTATTGAGAAGAAGGCGAAGTTTGATATCATGGACCTGAACTGTTTGCTG
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 7
aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttcttatgcttgcaa----tgaaactttaactccttt--ttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
||| | | | | | || | || | || | | || | || || | | || || | | | | | | ||| |||||||||||||| ||||||| |||||||||||| | | ||| |||| ||||| |||||| |||||||| |||| || ||| | ||
--aaatcctt--caagcaacatggaaataa-aacctatagctgt-taacttggattttctggtgtgtttattaagtcttatattctgctggatttgcctcaattagGTTAAAATGGCTGTACAGTACATGCGGAGGGTTATTGAGAAGAAGGCAAAGTTTGATATTATGAATCTGAACTGTTTGCAG
upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 5
aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttc--ttatgcttgcaa-tgaaactt---taactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
|| | ||| | | ||| || | | || | ||||||| || || || ||| | || | | ||| ||||||||||||| ||||||| || ||||||||||| | ||| |||| ||||| |||||| |||| ||||| || || ||| | |
-----tcagtggcagttaaact-tggattgtcttctagactgtgatacgttggacatttctagttttggttaagtctgagattttgctgatctgctttacaattagGTTAAAATGGCTGTACAATACATGCGGCGGGTTATTGAGAAGAAGGCAAAGTTTGATATCATGGACCTGAACTGTTTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattctagacattttcttatgcttgcaatgaaactttaactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
ctttaac putative branch site (score: 3)
ctttaactcctttttc CT-rich tract
tttttcaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttcttatgcttgcaatgaaactttaactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
- - - - - - - - - -cttatcc
- - - - - - - - - - - - - - - caatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaaac