Sequence
atgc intronic sequence ATGC exonic sequence...acttttatcatttttctgtttcttttattttctacacaatttgaatccctttgcacttcataatttgatcttgttgaattttattgtactgatgattcagGCAAGTCAGAGGTGTCGATTGTTGTTTACAAAGTTGGCGAATGTATGCAAGAACTGATTAAGTTGTGGAAAGAATATGATTTGTCTCATCCTGATAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08450.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------------------acttttatcatttttctgtttcttttattttctacacaatttgaatcc---ctttgcacttc----ataatttgatcttgttgaattttat-tgta----ctgatgattcagGCAAGTCAGAGGTGTCGATTGTTGTTTACAAAGTTGGCGAATGTATGCAAGAACTGATTAAGTTGTGGAAAGAATATGATTTGTCTCATCCTGATAAAAG
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gttttattcttttctttcatatttatgcatctcatttacacttccttcttaatgtgttgtttgttgtgattttgttatcatttgctaatctattgttggtacttggtactacttgtcgatggaagagagaaaattaaagcttgatgtttctgctaccctttcctttgcttgtccactatatataatttctggtctttcagGTAAAGTAGAAGTTTCTTCTGTTGTTTATAAAGTTGGCGAAAGCATGCAAGAACTGATAAAGTTGTGGAAGGAATATGAATCATCTCAATCTCAAATGGA
upper sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 1
acttttatcatttttctgtttcttttattttc--tacacaatttgaatccctttgcacttcataatttgatcttgttgaattttattgtactgatgattcagGCAAGTCAGAGGTGTCGATTGTTGTTTACAAAGTTGGCGAATGTATGCAAGAACTGATTAAGTTGTGGAAAGAATATGATTTGTCTCATCCTGATAAAAG
| ||| || | |||| | || | | | || || |||| | | || || | || || | || ||||| |||||| || |||| || || ||||||||| |||||||| ||| | |||||||||||||| ||||||||||| |||||||| || ||||| || |
tccactataatgtacttgttgatgaaatgaaaaggataagaggtggatatctttctattcattatgcccattatattatatgcga--gttctgatatttcagGTAAAGCAGAAGTCTCTTCTGTTGTTTATAAAGTTGGTGAAAGCATGCAAGAACTGATAAAGTTGTGGAAGGAATATGAATTATCTCAATCTCAAGTTGA
upper sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 3
acttt-tatcatttttctgtttcttttattttctacacaatttgaatccctttgcacttcataatttg-atcttgttgaattttattgtactgatgattcagGCAAGTCAGAGGTGTCGATTGTTGTTTACAAAGTTGGCGAATGTATGCAAGAACTGATTAAGTTGTGGAAAGAATATGATTTGTCTCATCCTGATAAAAG
|||| || | ||||| | | | | | |||| | | ||| | |||| || | | | || | | || | |||||| || ||| || || ||||||||| |||||||||||| | |||||||||||||| ||||||||||| ||| |||| | ||||| |||| |
acttggtactacttttcgatggaagagagaaaat-taaagcttgatgcttctgctactctttcctttgcatgtccactacatataattt-ctattatttcagGTAAAGTAGAAGTTTCTTCTGTTGTTTATAAAGTTGGCGAAAGCATGCAAGAACTGATAAAGTTGTGGAAGGAACATGAATCATCTCAATCTGAAATGGA
upper sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 2
--------------acttttatcatttttctgtttcttttattttc--tacacaatttgaatccctttgcacttcataatttgatct-tgttgaattttattgtactgatgattcagGCAAGTCAGAGGTGTCGATTGTTGTTTACAAAGTTGGCGAATGTATGCAAGAACTGATTAAGTTGTGGAAAGAATATGATTTGTCTCATCCTGATAAAAG
|| |||| || | |||| | || | | | || | |||| | ||||| || | | | | || || | || ||||| |||||| || |||| || || ||||||||| |||||||| ||| | ||||||||| |||| ||||||||||| | |||||| || |||
cattgtgtgatggtaccattataatgtacttgttgatgaaatgaaaaggataagaggtggacatctttcta-ttcatcatgtcctttatattatatgcaa--gTTCTGATATTTCAGGTAAAGCAGAAGTATCTTCTGTTGTTTATAAAGTTGGTGAAAGCATGCAAGAATTGATAAAGTTGTGGAAGGCATATGAATTATCT--------------Mapped 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|124781150|gb|EH871093.1|EH871093EST: TCAGGACAACGAAGGAGTACAAG
genomic: TCAGGACAACGAAGGAGTACAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccctttgcacttcataatttgatcttgttgaattttattgtactgatgattcagGCAAGTCAGAGGTGTCGATTGTTGTTTACAAAGTTGGCGAATGTATGCAAGAACTGATTAAGTTGTGGAAAGAATATGATTTGTCTCATCCTGATAAAAG
tactgat putative branch site (score: 2)
ttgttgaattttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttttatcatttttctgtttcttttattttctacacaatttgaatccctttgcacttcataatttgatcttgttgaattttattgtactgatgattcagGCAAGTCAGAGGTGTCGATTGTTGTTTACAAAGTTGGCGAATGTATGCAAGAACTGATTAAGTTGTGGAAAGAATATGATTTGTCTCATCCTGATAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - -ctgtttc
- - - - - - - - - - - - - - - - -acacaat