Sequence
atgc intronic sequence ATGC exonic sequencegtaatagcttgttcataactgcattcatagaagggttatatatacgtttgcatcttgtactgagttttaaatgcctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G70280.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G70280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g49770.1 (Oryza sativa), 3'ss of exon 4
------------gtaatagcttgttcataactgcattcatagaagggttatatatac-gtttgcatcttgtactgagttttaaatgcctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA---
|| || || | | | ||| || | || || | || | | || || || | ||| | ||| |||||||||||||| ||||| ||| | || ||||||||||| |||||||||||||| |||||||| ||||| | ||||||||| || ||
cttggtaaaattagaaaggcatgctgccatcatcatgcacatgtttgtctaatttgtagtaaacgggaaggtcttgacttggaagtgttctgacatttagGGGTTACAACTATTGCTGGGGGGAAATCAAGCAGA---GGAGGGCATGTTGATGGACCAAGTGATGATGCAAAATTTTCTACTGATTTTGAAGTCCGCTATAT
upper sequence: AT1G70280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G075260_T02 (Zea mays), 3'ss of exon 4
-------------gtaatagcttgttcataactgcat-tcatagaagggttatatatacgtttgcatcttgtactgagttttaaatgc--ctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA---
| ||| || | |||| | | | || || || || | |||||| ||| | | || |||||| ||| |||||||||||||| ||||| ||| | | || ||||||||||| || ||||||||||| || ||||| ||||| | ||||||||| || |||
tttggatgtttctgcaatca-ttatgcatactttctccttatctaatctcta-gtaaagaacgagctcttgt-ctgcctgacatattgtgttatgattcttagGGGTTACAACTATTGCTGGGGGGAAATCAGGCAGA---GGAGGGCATGTTGACGGACCAAGTGATGAGGCAAAATTTTCTACTGATTTTGAAGTCCGTTACAT
upper sequence: AT1G70280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G03880.1 (Glycine max), 3'ss of exon 4
-----------------------gtaatagcttgttcataactgcattcatagaagggttatatat-acgtttgcatcttgtactgag----tttta-------aatgcctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
| ||| |||| | || | ||| || | | | || || | ||| | ||||| || | | || | | | || || ||||| ||||| || || ||| | || || || ||||| ||||| ||||||||||| || || ||||| ||||||||||||||||||||
gcaagcattatgttatactctgagcaatcctttgtcctcttctaccccataagactccttttctctcacattagaatcagaggtgggagcttttttattgagttaaggtttctgttttcagGG-GTGACAACAATTGCTGGAGGAAAATGGAGCCGGGGAGGGGGTCATGTTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTTGTTTA
upper sequence: AT1G70280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G03810.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------gtaatagcttgttcataactgcattcatagaagggttatatatacgtttgcatcttgtactgagttttaaatgcctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
||| | | || || | ||| | || | || || | | ||| || | |||| || | | || | | | || || ||||| ||||| || || ||| | || || || ||| | ||||| ||||||||||| || || ||||| |||||||||||||| |||||
gcaagcattatgttatactctgagcaatcctttgtcctcctcagtcctctcccccataagacttcttttctactt---ctcacattagaatcgtaaat----tggagccttttatttagtt---aaggtttctgttttcagGG-GTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTGGTTTA
upper sequence: AT1G70280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0026g00330.t01 (Vitis vinifera), 3'ss of exon 4
------------gtaatagcttgt--tcataactgcattcatagaagggttatatatacgtttgcatcttgtactgagttttaaatgcctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
|||| || || | | | | | || | | | | | | || | || | | || ||| |||||||| ||||| ||||| || || || || |||||||| ||||| ||||||||||||||||||||||| |||||||||||||| || ||
gttgtttccagtgtaacagtttagagttgtgatcttctgtgttaaaca-tcacagaatgagagatcttcaatgctaatattgttgaattttctacctgcagGGGTTACAACAATTGCAGGGGGGAAGCTGGGCCGTGGAGGGGGGCATGTAGATGGGCCAAGTGAAGATGCAAAGTTTTCTAATGATTTTGATGTGGTGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggttatatatacgtttgcatcttgtactgagttttaaatgcctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
agttttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagcttgttcataactgcattcatagaagggttatatatacgtttgcatcttgtactgagttttaaatgcctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG