Sequence
atgc intronic sequence ATGC exonic sequence...gttttagatttgcacttctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G32330.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G32330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G115456_T01 (Zea mays), 3'ss of exon 1
--gttttagatttgcacttctaaagctgtcggatgaa--ttctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
| ||| |||||| || | ||| || | ||||||| | | | | || | | | | ||| ||||| ||||| || || |||||||| ||||| |||||||||||||| ||||| |||||| | ||||| |||||||| |||| | | || | || | |||||
tcacatatgatctgcactctactggcaattggaagatgctattttctcagcaaacaatttatattgcaccctaacgatgtcatctgtgcctttttac----cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: AT1G32330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
---gttttagatttgcacttctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
|| |||||||||| | |||| || | || || | | | || | | || | || ||||| ||||| || || |||||||| ||||| |||||||||||||| ||||| |||||| | ||||| || || || |||| | | || | || | |||||
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaa-cgatctcatcggtgccttcttac--cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: AT1G32330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G33920.1 (Glycine max), 3'ss of exon 2
---gttttagatttgcacttctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
|| || || | || || ||||||| | | | | | | ||||| | || || | ||| | | || || | ||||||||||||||||||||||| |||||| | ||||||||||| ||||| |||||||| || ||||| ||||||||||| ||||| || ||||||||||
tctgtgttttatata-acaactcaagctgtgtgccttttcatatgccct--gtcttttttttctcttcctttctaacatcgtcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
upper sequence: AT1G32330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G01990.1 (Glycine max), 3'ss of exon 1
------gttttagatttgcacttctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
| || | || | | | || || | ||| ||| || | | | | | | ||||| | | | | | || || | ||||||||||||||||||||||| |||||| | ||||||||||| ||||| |||||||| | ||||| ||||||||||| || || | ||||||||||
ataacaactcaagttgtgtgccttttcaga-gtgtgttgacctctgtcctgtcttttctttt----ttccttttc-taacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
upper sequence: AT1G32330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G13400.1 (Glycine max), 3'ss of exon 1
---gttttagatttgcacttctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
||| | |||| | | ||| || | | | | || || | | | | | ||| | | || | | || | | ||||| || |||||||| || |||||| | ||||||||||| ||||| || ||||| || ||||| ||||||||||| | | |||||| |||| |||||||
tttagtttgtttgtgca-tgccaaaactataatgttgtgtatgtcaaatcaaacatcgaccttttcctttctaat--atcatcaacaattcatcattaagcagGGATTTAGGAAGGTAGATCCAGATCGCTGGGAATTTGCAAATGAGGGATTTTTGAGGGGTCAAAAGCACTTGCTTAAGACTATAACTCGGCGGAAACCTG
upper sequence: AT1G32330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0012g01810.t01 (Vitis vinifera), 3'ss of exon 1
gttttagatttgcactt--ctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttg-atacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
||| |||| | | |||| | | | | || | | | || | ||| | | | |||| | || | |||||| |||||||||||||| ||||| | ||||||||||| ||||| || ||||| || ||||| || ||| | | |||| | ||||||||||||
--ttttattttgtatgtaatcaaagtctctttgtattctgctgattatagtttccctttcttccccatcctattttcctat-cttgtcactgtctgcaaacagGGATTCAGGAAGGTTGATCCAGACCGTTGGGAATTTGCAAATGAGGGATTTTTGAGGGGTCAAAAACACCTATTGAGGAGTATAAATCGGCGAAAACCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
tcttgat putative branch site (score: 4)
tgtcttttctt CT-rich tract
attttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttagatttgcacttctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
gttttag
- - - - - - - - -ctaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatcca