Sequence
atgc intronic sequence ATGC exonic sequencegtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23670.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 3'ss of exon 9
gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaa--aaactcccattcttctcaa-atactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
|| | || || | || | || || | | | | ||| ||| | | | | | | || || |||||| | ||||| || || || ||||||||||| || ||||| | ||||| ||||| ||||| ||||| || |||||||||||||| || || ||
----------------------------------------------gtatatcagaacttgttgatttc-ttatttcttctgtctttaggaaattcctaatgtaattattgttctaaatagGGGCCAAGAAGCTTGCTCAGATTCGAGAGAACAGCAATTTCTTCCGTTCAGAGCTTCAGAAAATGGGTTTTGAAGTTCTTGGAGACAATGACTCGCCGGT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 9
gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
||||| | |||| |||| || | | | || | ||| | ||| | | || | | | || | | | || || |||| || || || || ||| | || |||||||||||||| || || || | ||||| |||||||||| |||||||| || ||||||||||| || |||||
gtactagccttttcttct------------gcttcgaccctttcaatgcgctgcaggctatccatgtaagttttactttcaattcttatttattttggtttt----gatgtcttgcagGTGCCCAGAAACTTGCACGCATCCGTGAGAACAGCAATTTCTTTAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTCGGAGACAATGACTCTCCAGT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G030862_T01 (Zea mays), 3'ss of exon 8
gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtc-actgagcacaatcta--atcaggtcatgactcataacctaaaaactcccattcttctcaaatactg--aacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
| ||| || | || || | | || || ||| | || | ||| | | | || | | | | | | ||| | | || |||| || || || || || | || ||||||||||||||||| ||| || | ||||| |||||||||| |||||||| ||||| ||||| || || || ||
------------gtccctccccttttcgttcgc-gactatatatgtgtccaactagaataatgttgtactgaataatccttttttttttgtttttttgcttgcttgggatgtgttgcttgcagGTGCCCAGAAACTGGCGCGCATCCGTGAGAACAGCAACTTCTTCAGGTCAGAGCTCAAGAAGATGGGCTTTGAGGTTCTTGGTGACAACGACTCTCCTGT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
|| | | |||| || ||| || | || ||| || | || || || | | || || | | || | |||||| | ||||| || ||| || ||||||||||| || ||||| | ||||| ||||| ||||| |||||||| |||||||| |||||||| || ||
-----------------gtacaacataaagaatt--ccaaattcttacaccttaccagtttcttat-acttcctgccttgt----tgaatgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 9
gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
||||| | ||| | ||| ||| | | ||| | | | | || | ||| | || | ||||| | | ||| |||| || || ||||| || ||| | || ||||||||| | || || ||| || | || || |||||||||| |||||||| ||||| ||||||||||| || ||
gtactaaaccagctttttt-taacacttttatttgtgcccttttcgtttgc------------agctgtgttagtgttca--attaaatgtttttttttcttgtgatatattgaa--gGTGCCCAAAAACTTGCACGCATCCGTGAGAACGGTAATTTCTTCAGGTCCGAACTCAAGAAGATGGGTTTTGAGGTTCTTGGCGACAATGATTCTCCTGT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 9
---------gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagca-caatctaatcaggtcatgact-cataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
| ||| | || | | | | || || | | | || | || ||| ||||| || | | || | | || | | || | ||| || || || || ||| ||| || ||||| ||||||||||| || | || ||||||||||||||||||||||| ||||| || |||||||| |||||
gtttggctggcactag-ttctgctctttgctttgcatttgtattgtttgatgattttttatgtgcatcaatccaaataatattcgtctactttgtttaccgtgcattgaagtaagttttttctatatagGTGCCCAGAAACTTGCACAAATTCGAGAGAATAGCAACTTTTTTAGGTCAGAACTGCAGAAGATGGGATTTGAGGTTCTTGGGGATAATGATTCTCCAGT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 9
--gtactcgattttttttct-caccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaaa--aactcccattcttctcaaata---ctgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
| | | |||| | | || | ||| | | ||| | | | || || | || | || || | | || |||| | | | || | ||| || || || || ||| ||| || || || |||||||||||| || | || |||||||||||||||||||||| ||||| || |||||||| |||||
gtttggctggcactagttctgctctttgctttgcatttgtatttgatggttttttacgtgca-tcaatccaaataatattcatctactttgtttaccttgcattgaagtaagttgtttctatatagGTGCCCAGAAACTTGCACAAATTCGAGAAAATAGCAACTTTTTCAGGTCAGAATTGCAGAAGATGGGATTTGAGGTTCTTGGGGATAATGATTCTCCAGT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
-----gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
|| | | || | | || |||| | | ||| || | | | | | ||| || | | | | | ||| | | ||| || ||||| || ||| |||||||||||| |||||||||||| || | || ||||||| ||||| |||||||| ||||| || ||||| || |||||
gtaggataaataaatcttctgtcatgcttggttttaacttctatt-cttgaatctttaggt----ttcagactctccattgctttaattgtttttgattttagtgctcttgtgt-ccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
gtactcgattttttttctcaccgtgtcattaattg-gcctcatttgggtcactgagcaca-atctaatcaggtcatg-actcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
| | | || | |||| || | | ||||| | || | | | |||| | || | || || || | | || || | | ||||| | |||||| || || | ||| |||||||||||||||| ||||||||| | | || |||||||||||||| |||||||| |||||||| |||||||| || ||
---gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatct--tgagcttatttgcttattgtttga----tctgcttttgtttaaatatt----agGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86059362|gb|DR355119.1|DR355119EST: AATTATATCTGCCATTAAAGTTATTCTGGGAGAGGATGGTTCAAACCGAG GGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTG
genomic: AATTATATCTGCCATTAAAGTTATTCTGGGAGAGGATGGTTCAAATCGAGgtactcgatt ... tactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcaggtcatgactcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
taaaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA