Sequence
atgc intronic sequence ATGC exonic sequencegtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 15
gtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
| | | | ||| || |||| | || | || | || | ||||| | || | | | |||| |||||| ||||| || || | ||||| ||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||| |||
atgtttcatacaggatcatgtattcttattacatgtagcatcaacttgacagtggcttg-tactatgtataaaggcaaaattttgtgttttaaaat----tgcagGAGAAGGTACAGGGCTTCTTCGCCTCCATAGTACATACCGTCATGATCTCAAGATTTACAGCTCTGATGAGGGTCGTGTGCAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 19
gtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
|| | | |||| | || || |||| | ||| | || || || | ||||| | || | | | | || |||||| ||||| || || | ||||| ||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||| |||
gtttcata-caggatc-atgcattcttattacatgtaacatcaacttgacagtgtcttg-tagtatgtataaaggcaaatttttgtgtggtttaaaat--tgcagGAGAAGGTACAGGGCTTCTTCGCCTCCATAGTACATACCGTCATGATCTCAAGATTTACAGCTCTGATGAGGGTCGTGTGCAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 15
gtaagggaacttgatctacttatatttgttactttccacaggagtt-tagtgtactcgtgacgatcagt-atattttctaagtatctcacgatgaaatggca-----tgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
|||| || | | | | ||| || | || || | || | |||| || | || | | | || | || | | ||||| ||||| || || ||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||||| ||||| |||
-----------tgataggttt-caaatatgatttttcattgttcttgtaatatagacatgacaatggattgtaccatgcatgacatgcaaattaaattcttaaatgtcgcagGAGAAGGTACAGGGCTGCTTCGCCTCCATAGCACATACCGTCATGATCTTAAGATATACAGCTCTGATGAGGGTCGTGTGCAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 17
gtaagggaacttgatctacttatatttgttactttccacaggagtt-tagtgtactcgtgacgatcagtatattttctaagtatctcacga--tgaaatggca-----tgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
| | | || | || | | ||| || | || || | || | |||| | ||| | | | | | | | | || | | || ||| ||||| || || ||||||| |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||||| |||
------------ggtatgttt-caattatgatttttcattgttcttgtaatatagacatgacaaacagattgtaccatgcatgacatgcaaattaaattcttaaatgttgaagGAGAAGGTACAGGGCTGCTTCGCCTCCATAGCACATACCGCCATGATCTTAAGATATACAGCTCTGATGAGGGTCGTGTGCAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 17
gtaagggaacttgatctacttatatttgttactttccacaggagtttagtg-tactcgtgacgatcagtatattttctaagt-atctcacgatgaaatggcat-gcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
| | | | | || ||| | | | | || | ||| || ||| | | |||| | | | | || ||| || ||||||||||| ||||| ||||||| || |||||||| || |||||||| || |||||||||||||| || ||||| ||||| |||
--------aatccttttgtgtggatgaattaatacctgtggtcttcctctgcttctcttggtgatttttttttttttttttttaaattgttattgtatgtaattgcagGTGAAGGCACTGGCCTGCTTCGCCTTCATAGTACTTATCGTCATGATCTAAAAATTTACAGCTCAGATGAGGGTCGTGTACAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 17
--------------------------------------------------------gtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
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gtaaataccacggattagctgcatggaggaaactactacttctaagtgttgcacatgctagataagaaagtaaatttgacagagttgcacttaatgtagacatactgcattctggttcatttgaaaagcacatccatgtga-atcctgatatggattgcagGAGAGGGGACTGGTTTGCTGCGACTCCATAGTACTTATCGGCATGACTTGAAAATCTACAGTTCCGACGAAGGGAGGGTGCAGMapped 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|124881521|gb|EH960423.1|EH960423EST: CAGGCAGAAGAACTTGGTAGATACTTTCGAAACAATATGTATCCAG GTGAAGGGACTGGTTTGCTTCGTCTCCA
genomic: CAGGCAGAAGAACTTGGTAGATACTTTCGAAACAATATGTATCCAGgtaagggaac ... tggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
atctcac putative branch site (score: 3)
tatattttctaagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC