Sequence
atgc intronic sequence ATGC exonic sequence...agtgtctgaacgcaatgtatgatcgtttgttgaatatgtgttatgtttatgaaatgagtttcaacccacatttttaaagtatctgctttaaaaactacagGTTCTGGCAGTTCGGGCTGGCAAGCACCAGAGCAGCTTCTACAAGGTCGTCAAACTCGTGCAGTCGATATGTTTAGTTTAGGTTGTGTCATCTTTTACAC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G17520.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G17520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G162167_T02 (Zea mays), 3'ss of exon 2
---------agtgtctgaacgcaatgtatgatcgtttgttgaatatgtgttatgtttatgaaatgagtttcaacccacatttttaaagtatctgctttaaaaactacagGTTCTGGCAGTTCGGGCTGGCAAGCACCAGAGCAGCTTCTACAAGGTCGTCAAACTCGTGCAGTCGATATGTTTAGTTTAGGTTGTGTCATCTTTTACAC
| | | | | | | ||| | | ||| | | || | || ||| | | | ||||| || | | ||| |||| ||| || || |||||||||||||| || ||||||| || |||||||||||||||||| | ||| | |||||||| || || | || || ||
gtacagaggttcacccttgctgagggaaatacattctgtatgttgtttgtcacactgctgtagtgtatttttagctagcagtttaat---ccttggtggtatactccagGAATTGGAAGCTCTGGCTGGCAAGCACCCGAACAGCTTCGTCATGGTCGTCAAACTCGTGCAATGGATCTTTTTAGTTTGGGCTGCCTTATTTTCTATTG
upper sequence: AT2G17520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G21480.1 (Glycine max), 3'ss of exon 5
agtgtctgaacgcaatgtatgatcgtttgttgaata-tgtgttatgtttatgaaatgagtt--tcaacccac-atttttaaagta--tctgctttaaaaactacagGTTCTGGCAGTTCGGGCTGGCAAGCACCAGAGCAGCTTCTACAAGGTCGTCAAACTCGTGCAGTCGATATGTTTAGTTTAGGTTGTGTCATCTTTTACAC
|| || | | | || |||||||||| | || | | || ||| || | | | ||| | | || | | | | ||||| ||||||||| || ||||||||||||||||| ||| | |||| |||||||| || ||||| ||||| |||||||||||||||||| |||||| |
-----cttaattgagtagcttgtcttttgttgaatcctacattttaatc-tgcaatactttaattagtttattattctcgtactaaggtttactggcttattgcagGTGGTGGCAGTTCAGGTTGGCAAGCACCAGAGCAACTTGTTGAAGGACGTCAAACACGGGCAGTAGATATATTTAGTTTAGGTTGTGTCCTCTTTTTCTG
upper sequence: AT2G17520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G32970.1 (Glycine max), 3'ss of exon 3
agtgtctgaac-gcaatgtatgatcgtttgttgaat----atgtgttatgtttatgaaatgagtttcaacccacatttttaaagtatctgctttaaaaactacagGTTCTGGCAGTTCGGGCTGGCAAGCACCAGAGCAGCTTCTACAAGGTCGTCAAACTCGTGCAGTCGATATGTTTAGTTTAGGTTGTGTCATCTTTTACAC
| ||| | || || | | | | | || || || || || || | || | | | | | | | ||| |||| | ||||| ||||||||| || ||||| |||||||| || ||| | | ||| |||||||| || ||||| ||||| |||||||||||||||||| | |||| |
--agcttgagcagcttggttttgttgaatcctacattttaatctgcaatactttataattagtttattattctcgtgctaaggtttactggcttaa---ttgcagGTGGTGGCAGTTCAGGTTGGCAGGCACCAGAACAACTTGTTCGAGGACGTCAAACCCGGGCAGTAGATATATTTAGTTTAGGTTGTGTCCTTTTTTTCTG
upper sequence: AT2G17520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G36200.1 (Glycine max), 3'ss of exon 2
agtgtctgaacgcaatgtatgatcgtttgttgaatatgtgttatgtttatgaaatgagtttcaacccacatttttaaagtatctgctttaaaaac-tacagGTTCTGGCAGTTCGGGCTGGCAAGCACCAGAGCAGCTTCTACAAGGTCGTCAAACTCGTGCAGTCGATATGTTTAGTTTAGGTTGTGTCATCTTTTACAC
||| | | || | | | | || | | | | | | | || | | | | || | | | | | | | |||| | | ||| | ||| ||||| || ||||||||||| ||||| ||| | ||||| |||||||| || || || ||| | |||||||||||||| || |||||| |
-gtgagtagaagcgttaattttacaggtcttaactcttaatcaattctttgttcttattcttaatct-tacaataaggttcaattccttaattgcatgtagGCTGTGGAAGTTCAGGGTGGCAAGCACCGGAGCAACTTGTTCAAGGACGTCAAACACGAGCTGTGGATTTATTTAGTTTAGGTTGCGTTCTCTTTTTCTG
upper sequence: AT2G17520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0031g02180.t01 (Vitis vinifera), 3'ss of exon 4
agtgtctgaacgcaatgtatgatcgtttgttgaatatgtgttatgtttatgaaatgagtttcaacccacatttttaaagtatctgctttaaaaactacagGTTCTGGCAGTTCGGGCTGGCAAGCACCAGAGCAGCTTCTACAAGGTCGTCAAACTCGTGCAGTCGATATGTTTAGTTTAGGTTGTGTCATCTTTTACAC
| | | | | | | | | || | | || |||| | | | | | ||| | || | |||||| |||||||||||| ||||| ||||| ||||||||||| || || || ||||| || ||||| ||| |||||||||||||||| || |||||| |
atttcactggcccccttcacaacttagcaattcacatataaatcataagtggttattatttctattgagttcagtgatttatttatgactcaatttgcagGTTATGGCAGTTCGGGTTGGCAGGCACCTGAGCAGCTTCTTCATGGACGCCAAACACGAGCAGTAGATTTGTTTAGTTTAGGTTGCATCCTCTTTTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatgaaatgagtttcaacccacatttttaaagtatctgctttaaaaactacagGTTCTGGCAGTTCGGGCTGGCAAGCACCAGAGCAGCTTCTACAAGGTCGTCAAACTCGTGCAGTCGATATGTTTAGTTTAGGTTGTGTCATCTTTTACAC
acatttttaaagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgtctgaacgcaatgtatgatcgtttgttgaatatgtgttatgtttatgaaatgagtttcaacccacatttttaaagtatctgctttaaaaactacagGTTCTGGCAGTTCGGGCTGGCAAGCACCAGAGCAGCTTCTACAAGGTCGTCAAACTCGTGCAGTCGATATGTTTAGTTTAGGTTGTGTCATCTTTTACAC
- - - - aacgcaa
- - - - - - - - - - - - - - - - - - - - - - - - atgaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaccc