Sequence
atgc intronic sequence ATGC exonic sequencegtgagtagactattcaaaagagctcatacattgtctttgtaatgtaaaactatgtaatgttttaatgaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTTCATCATGCCGGGATACCGTCTATAGACATGTACTATGGAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54720.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 4
---------------------gtgagtagactattcaaaagagctcatacattgtctttgtaatgt-aaaactatgtaatgt---tttaatgaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTTCATCATGCCGGGATACCGTCTATAGACATGTACTATGGAGCAG
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tattataataatgtctgtttttcccattttttttcaaagtgggtttcaactttgtcgtggtatcctcattgctaagccacttttgttttgttggttgcagATTCAGAGGCTCAGTGGAGTAGATTCCGATTTTGCTCCATTTGTGCAACACGCAGGGGTTCCATCCATTGACATGTATTATGGAAGAG
upper sequence: AT3G54720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G36430.1 (Glycine max), 3'ss of exon 4
------------------gtgagtagactattcaaaa--gagctcatacattgtc------tttgtaatgtaaaactatgtaatgttttaatgaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTTCATCATGCCGGGATACCGTCTATAGACATGTACTATGGAGCAG
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tatgataatgttgggtttttgccatgcttttttcaaactgggtttcaattttgttgtgatgtcttcattgcttagccacttt-tattttattggattgcagATTCAGAGGCTCAGTGGAGTTGATTCTGATTTCGCTCCATTTGTGCAACACGCAGGGGTTCCATCCATTGATATGTATTATGGAAGAG
upper sequence: AT3G54720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 4
------------------------gtgagtagactattcaaaagagctcatacattgtctttgtaatgtaaaactatgtaatgttttaa-tgaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTTCATCATGCCGGGATACCGTCTATAGACATGTACTATGGAGCAG
|| | | | || | || || | | | | | |||| | | | ||| || || | |||||||||||||||||||| |||| |||||||||||| | || | || ||||| ||| | || ||| | || | ||||||||| ||
gctttataaattatggctttggatatgtcaaaatttatctttgttttttctatatggattgtatgaagtaattattgggattgtcttggctggattgcagATTCAGAGGCTAAGTGGAGTGGATTCTGATTTTGCTCCACTTTTGCAACATGCAGGGGTTCCTTCTGTTGATTTATACTATGGAAGAG
upper sequence: AT3G54720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0319g00060.t01 (Vitis vinifera), 3'ss of exon 3
------------------------gtgagtagactattcaaaagagctcatacattgtctttgtaatgtaaaactatgtaatgttttaa-tgaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTTCATCATGCCGGGATACCGTCTATAGACATGTACTATGGAGCAG
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gctttataaattttggctttggatatgtcaaaatttatatttgttgtttctatatggattgtatgaagtaattattgggattgtcttggctagattgcagATTCAGAGGCTAAGTGGAGTGGATTCTGATTTTTCTCCACTTTTGCAACATGCAGGGGTTCCTTCTGTTGATTTATACTATGGAAGAG
upper sequence: AT3G54720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0327g00020.t01 (Vitis vinifera), 3'ss of exon 3
------------------------gtgagtagactattcaaaagagctcatacattgtctttgtaatgtaaaactatgtaatgttttaat-gaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTTCATCATGCCGGGATACCGTCTATAGACATGTACTATGGAGCAG
|| | | | | | | || || | | | | | |||| | | | ||| | | | | |||||||||||||||||||| |||| |||||||||||||| || | || ||||| ||| | || ||| | || | ||||||||| ||
gctttataaattatggctttggatatgtcaaaatttatatttgttgtttctatatggattgtatgaagtaattattgggattgtcatggttggattgcagATTCAGAGGCTAAGTGGAGTGGATTCTGATTTTTCTCCACTTTTGCAACATGCAGGGGTTCCTTCTGTTGATTTATACTATGGAAGAG
upper sequence: AT3G54720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0032g00670.t01 (Vitis vinifera), 3'ss of exon 4
------------------------gtgagtagactattcaaaagagctcatacattgtctttgtaatgtaaaactatgtaatgttttaa-tgaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTTCATCATGCCGGGATACCGTCTATAGACATGTACTATGGAGCAG
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gctttataaattatggctttggatatgtcaaaatttatctttgttgtttctatatggactgtatgaagtaattattgggattgtcttggctggattgcagATCCAGAGGCTAAGTGGAGTGGATTCTGATTTTGCTCCACTTTTGCAACATGCAGGGGTTCCTTCTGTTGATTTATACTATGGAAGAGMapped 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|164193908|gb|ES083966.1|ES083966EST: TGCAGTTAGGCTTGACAGTGGAAGAGACATTTAAGTCTCAAAATAACATT ATTCAGAGGCTAAGTAGAGTAGATTCTGATTTT-CCGGTTTTCTT
genomic: TGCAG-TAGGCTTGACAGTGGAAGAGACATTTAAGTCTCAAAATAACATTgtgagtagac ... tgaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctcatacattgtctttgtaatgtaaaactatgtaatgttttaatgaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTTCATCATGCCGGGATACCGTCTATAGACATGTACTATGGAGCAG
ttttaat putative branch site (score: 3)
taatgtaaaactatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtagactattcaaaagagctcatacattgtctttgtaatgtaaaactatgtaatgttttaatgaactgcagATTCAGAGGCTAAGTAGAGTAGATTCTGATTTTTCCGGTTTTCTTCATCATGCCGGGATACCGTCTATAGACATGTACTATGGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG