Sequence
atgc intronic sequence ATGC exonic sequencegtaacatcatctctaagcaaagagccttgaaatgtttccatccatatggtagagactaagttgttggaccttttaattagGCTGCTGTGGAAGAAGGTATTGTTGTTGGCGGAGGATGTACTCTGCTAAGACTTGCATCGAAAGTGGACGCTATTAAAGAGACTCTAGCAAACGATGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56500.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 10
---------------------------------------gtaacatc--atctctaagcaaagagccttgaaatgttt--ccatccatatggtagagactaa---------gttgttggaccttttaa--------------ttagGCTGCTGTGGAAGAAGGTATTGTTGTTGGCGGAGGATGTACTCTGCTAAGACTTGCATCGAAAGTGGACGCTATTAAAGAGACTCTAGCAAACGATGAAG
||| | | |||| || | || | | || || || || | || | ||||| |||| || | |||||||||| || ||||||||||||||||| ||||| || ||||| || ||||| ||| | | ||| ||||| || || || | || | || |||||
gttagtctgttgttataactgctttgagatagaaatagattaatgtttgcttcttaaggaagaaaaattaaggtagtttgttgctcactgagttgatatcaacgttcttctggctttggatctttaaaccgcttcctctttgtcagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGC
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
---------------------------------------------------------gtaacatcatctctaagcaaagagccttgaaatgtttccatcca-------tatggt-----agagactaagttgttggaccttttaattagGCTGCTGTGGAAGAAGGTATTGTTGTTGGCGGAGGATGTACTCTGCTAAGACTTGCATCGAAAGTGGACGCTATTAAAGAGACTCTAGCAAACGATGAAG
| || | || | | || | | | |||| | || | |||| | | || ||| | || | ||||||||||| || ||||||||||||||||| |||||||| || || | | |||||| | ||||| || || || || || || || | ||||||||
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 9
gtaacatcatctctaagcaaagagccttgaaatgtttcca---tccatatggtagagactaagttgttggaccttttaattagGCTGCTGTGGAAGAAGGTATTGTTGTTGGCGGAGGATGTACTCTGCTAAGACTTGCATCGAAAGTGGACGCTATTAAAGAGACTCTAGCAAACGATGAAG
|| | | | | || || | || ||| || | || || | || |||||| || || |||| ||||| || ||||||||||||||||| || || || ||||| || ||||||||||| || ||||| || || || || | || | || |||||||
---gtgtccttttctttcccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttg-actttc-----agGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgaaatgtttccatccatatggtagagactaagttgttggaccttttaattagGCTGCTGTGGAAGAAGGTATTGTTGTTGGCGGAGGATGTACTCTGCTAAGACTTGCATCGAAAGTGGACGCTATTAAAGAGACTCTAGCAAACGATGAAG
cctttt CT-rich tract
ttttaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatcatctctaagcaaagagccttgaaatgtttccatccatatggtagagactaagttgttggaccttttaattagGCTGCTGTGGAAGAAGGTATTGTTGTTGGCGGAGGATGTACTCTGCTAAGACTTGCATCGAAAGTGGACGCTATTAAAGAGACTCTAGCAAACGATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA