Sequence
atgc intronic sequence ATGC exonic sequencegtttgttttgtccattattatatttccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01770.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------gtttgttttgtccattattatatt-tccttgtaattgtatgatttgg----tatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
| |||| ||| | || || | | || | | |||| ||| | || || | | || | || | | || | | |||| ||| |||||||||| |||||| ||||||| ||||| || ||||| |||||||| ||||| | ||||| || ||||| ||| |||||||||||||||
gtgctattaaccgtctttgctttttttgaatgatctaatactttggacatcaacattttgttggcattgttatgttgtttgagaattatcacttcagtaccatcactt-tgttcatttccttactcaaaccagCCGAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTC
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------------------gtttgttttgtccattattatatttccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
| || |||| | | | || || | || | | |||| || | | | | | |||| | | ||| | | |||| |||| ||| |||||||||||||||| ||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||| ||||| ||||| |||||||
gtatctggatttttttttgtaataactctgatgcaagttctttctaaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaata-atagtaatacgatgg-actattttataagttttgagcttacctgatgaagtatgtggttgttcttt---cagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------------------------gtttgttttgtccattattatatttccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
| || |||| | | | || | | ||| | | |||| || | | | | | ||| | | ||| | | |||| ||| ||| |||||||||| ||||| ||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||||||||| ||||| |||||||
gtgtctggattatttttttgtaataactctgatgtaaagttctttctgaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatactaa--ggaatattttataagttttgagcttacctgaagaagtatgtggttgttcttt---cagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------------------------gtttgttttgtccattattatatttccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
||| | | | | || || || || ||| || | |||| | || | | ||| | | || | ||| | |||||||| | || ||||||||||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| |||||||||||||| || ||||||||||
gtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgcttgggtacttgaaacgagcatttagagtacctagaagaatgttgtgctg--gttttatcatctcatatgcc--cagttacgacattgatgtctat-acaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 9
-gtttgttttgtccattattatattt--ccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttact-----ctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
||| || | | || | ||| || ||||||| | | || | | | | | |||| | ||| | | || ||| | |||| ||| | |||||||| |||||| ||||||| ||||| || ||| |||| ||||| ||||||| |||||||||||||||||| | ||||| ||||| |
tgttgtcttgatgtttctttgtttttatccatgtaatt-tttttttgaatgctagtagcattctctggatactacttactgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 3'ss of exon 9
--gtttgttttgtccattattatatttccttgtaattgtatgatttggtatga-tgtctgtcttgttgataatgcttg----ttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
|| ||||| ||| |||||| | | ||| | || | | || | | | ||| | || |||| ||| || | | |||| ||| | |||||||| |||||| |||||||||| ||||| |||||||| ||||| ||||| ||||||||||| ||||| | ||||| |||||||
tttttcgtttttaaaatttttatatcatttaattattatttgtgtcgaaatcagtagcaaatttgaaaacaagacttgatttttagcctttctattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCTTTCGAGGTGTGGCTGGAGCATGGTTCTGAAAGGAAGAAGCCACCTGAGCAACTTCCTATCGTTCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatttggtatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
tgttgat putative branch site (score: 4)
cttgttactctccttt putative PPT
ttgataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttttgtccattattatatttccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG