Sequence
atgc intronic sequence ATGC exonic sequence...actaggcaggcattatatattattctgtattgattttagaatttggtacttattcctgcaccattagcttctcgtcatatttcactggtccattttgcagGCCAAGCTTGCTAAGCTTCGGAGGGACCTTCTTGCACCGCCTACCAAAGGTGGCGGTGGTGGTGCTGGAGAAGGTTTTGATGTGACTAAAAGTGGAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39520.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 2
actaggcaggcattatatattattctgtattgattttagaatttggtacttattcctgcaccattagcttctcgtcatatttc--actggt--ccattttgcagGCCAAGCTTGCTAAGCTTCGGAGGGACCTTCTTGCACCGCCTACCAAAGGTGGCGGTGGTGGTGCTGGAGAAGGTTTTGATGTGACTAAAAGTGGAGATT
| | | | || | |||| | |||| ||| || | | | | | || | ||| | || | |||| | || || ||||| || ||||| || | || | || | || | || | |||||||||| ||||| |||||||| || || ||||||||||| ||||||||||||
-tcacatattcttgctactagaacctgtgtactttttg---tttagtttaatctgccacttctacaaattattgtctttttcctaactgttttcctcttatcagGCTAAACTTGCAAAATTACGCCGTGAGTTGCTGACTCCTACATCCAAAGGTGGTGGTGGCGGTGCTGGCGAGGGATTTGATGTGACAAAAAGTGGAGATG
upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 2
-actaggcaggcattatatatt-attctg-tattgattttagaatttggtacttattcctgcaccattagcttctcgtcatatttcactggtccattt-tgcagGCCAAGCTTGCTAAGCTTCGGAGGGACCTTCTTGCACCGCCTACCAAAGGTGGCGGTGGTGGTGCTGGAGAAGGTTTTGATGTGACTAAAAGTGGAGATT---
| | | ||| ||||| ||| || | || || | || | || || | | || | || | | || | | | | || | ||| |||| || ||||| || | ||| |||| | || | || | |||||||||| ||||||||| || ||||| ||||||||||| || |||||||||
cttcatgttgatatttgatatttattatgacactgtactttg--ttgagctgatactctttgat-atcaactgagc-ttatgtcttaattgttcgtttgcctagGCTAAACTTGCAAAATTGCGGCGGGAGTTGCTCACTCCAACATCCAAAGGTGG---TGGTGGTGCAGGTGAAGGATTTGATGTGACGAAGAGTGGAGATGCAC
upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 2
---actaggcaggcattatatattattctgtattgattttagaatttggtact--tattcctgcaccattagcttctcgtca-tatttcactggtccattttgcagGCCAAGCTTGCTAAGCTTCGGAGGGACCTTCTTGCACCGCCTACCAAAGGTGGCGGTGGTGGTGCTGGAGAAGGTTTTGATGTGACTAAAAGTGGAGATT---
| || || | || ||| | | | | | || | || | || || || | | | || | ||||| | ||||| || | || ||| | |||||||| || ||| |||| | | |||| | || ||| |||||||| |||||||||||||| ||||||||||| ||||
ccccttctttgagcttttcaagttcctcttctgttttcctgtattctgttgctgtttttgttgaggggttgattcattattggtaaatatctggtgc------cagGCTAAATTAGCAAAGTTGCGGAGGGAACTCCTTACACCTTC-ATCAAAAGGAGC--TGGAGGTGCTGGTGAAGGTTTTGATGTTACTAAAAGTGGGGATTCAA
upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G15180.2 (Glycine max), 3'ss of exon 2
---actaggcaggcattatatattattctgtattgattttagaatttggtacttattcctgcaccattagcttctcgtcatatttcactggtccattttgcagGCCAAGCTTGCTAAGCTTCGGAGGGACCTTCTTGCACCGCCTACCAAAGGTGGCGGTGGTGGTGCTGGAGAAGGTTTTGATGTGACTAAAAGTGGAGATT---
| || || | || ||| | | | | | || | || || || || | || | | || | ||||| || || || ||||| |||||||| || ||| |||| | | |||| | || ||| |||||||| |||||||||||||| ||||||||||| ||||
ccccttctttgagcttttcaagttcctcttctgttttcctgtattctgttgct-gtttttgttgaggggttgattcattattggtaaatgtctggtgc--cagGCTAAACTAGCAAAGCTGCGGAGGGAACTCCTTACACCTTC-ATCAAAAGGAGC--TGGAGGTGCTGGTGAAGGTTTTGATGTTACTAAAAGTGGGGATTCAA
upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 3'ss of exon 2
actaggcaggcattatatattattctgtattgattttagaatttggtacttattcctgcaccattagcttctcgtc-atatttcactggtc-cattttgc-agGCCAAGCTTGCTAAGCTTCGGAGGGACCTTCTTGCACCGCCTACCAAAGGTGGCGGTGGTGGTGCTGGAGAAGGTTTTGATGTGACTAAAAGTGGAGATT---
|| ||| | ||| || | || | | ||| || ||||| | ||| | || || ||| || | | ||| |||| || ||||| || || || ||||| || |||||||| | | |||| | | | ||||||| |||| |||||||||||||| ||||||||||||||||
---tggattgcagtgtattttttaagaatttcttgatgtgtttttttaattattgattttccaatgaaaaacaatctgaatgtcattgattgtctcctgctagGCTAAACTTGCAAAACTACGAAGGGAACTCCTTGCACC-CTCATCAAAAG--GTGCTGGTGGTCCTGGTGAAGGTTTTGATGTTACTAAAAGTGGAGATTCAA
upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S26_115V6.1 (Physcomitrella patens), 3'ss of exon 2
--------actaggcaggcattatatattattctgtat-tgattttagaatttggtacttattcctgcaccattagcttctcgtcatatttcactggtccattttgcagGCCAAGCTTGCTAAGCTTCGGAGGGACCTTCTTGCACCGCCTACCAAAGGTGGCGGTGGTGGTGCTGGAGAAGGTTTTGATGTGACTAAAAGTGGAGATT---
| || |||| || | | || | || ||| || | || || | |||| | ||| || | |||||| |||| || | |||||| | || | || |||| || || || | ||||| || || || |||||||||||||| ||||||||||||||||
cagttcaaagagttttggtattacatcaaagctcggatgtaatcctaggcttcaat---taatcaagtctgattaaaagggtgacatgttacgt------attttgtagGCAAAATTGGCTAAGTTGCGACGAGAAATTCTGGCGCCACCGTCTTC---CAAAGGTGGAGGAGCAGGCGAAGGTTTTGATGTCACTAAAAGTGGAGATTCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacttattcctgcaccattagcttctcgtcatatttcactggtccattttgcagGCCAAGCTTGCTAAGCTTCGGAGGGACCTTCTTGCACCGCCTACCAAAGGTGGCGGTGGTGGTGCTGGAGAAGGTTTTGATGTGACTAAAAGTGGAGATT
tccatttt CT-rich tract
tcatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actaggcaggcattatatattattctgtattgattttagaatttggtacttattcctgcaccattagcttctcgtcatatttcactggtccattttgcagGCCAAGCTTGCTAAGCTTCGGAGGGACCTTCTTGCACCGCCTACCAAAGGTGGCGGTGGTGGTGCTGGAGAAGGTTTTGATGTGACTAAAAGTGGAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - -aatttgg