Sequence
atgc intronic sequence ATGC exonic sequencegtttgcatatgcatgatcaatctgttcttcttcttttttcgtttgtgactgagaaagattctgagattaattgatatgtatgaagGTCTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55020.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 14
-----------------------gtttgcatatgcatgatcaatctgttcttcttcttttttcgtttgtgactgagaaagattctgagattaattgata-tgtatgaagGTCTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGC
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gtgtagtagctaccaatatgttgctctgaataaaccttgtca--ctactacatcatgccttttactactggtttatctag-ttataaactaactaggtaatgcatgtagGTCCTGATGCGTGTAGAGCAAGAACAGAAAGTCACTGAGGATGCGCGCATATTCGCTGAGCAAGATGCTGCTGCTCAGAAATATGCTGCACATGTGCTCC
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 14
gtttgcatatgcatgatcaatctgttcttcttcttttttcgtttgtgac-tgagaaagattctgagat--taattgatatgtatga-agGTCTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGC
| | |||||| | ||| || | | || | || || || ||| | || | | ||| ||||||||||||||||||||||||| || ||||| || || ||||| || | ||||||||||| ||||||| || || ||||||||||| |||||| | |
---------gtctcattttgtctgtttgtattcattctcgggttaacatatgttttctcttgtgtgatgtgagtttttgttgctgatagGTCTTGATGCGGGTGGAGCAAGAGCAAAAGGTGACTGAGGATGCTCGTAGGTTTGCTGAGCAAGATGCAGCCGCACAAAGATATGCTGCGCAAGTCCTTC
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 14
gtttgcatatgcatgatcaatctgttcttcttcttttttcgtttgtgactgagaa---agattctgagattaattgatatgtatga-agGTCTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGC
| | |||||| | ||| || || | | | | | ||| || | || | | ||| ||||||||||||||||||||||||| || ||||| || || ||||| || | ||||||||||| ||||||| || || ||||||||||| |||||| | |
--------gtctcatttttgtctgtttgtattcattcttgggataaaatatgctttctcgtatgtgacatgagtttttgttgctgatagGTCTTGATGCGGGTGGAGCAAGAGCAAAAGGTGACTGAGGATGCTCGTAGGTTTGCTGAGCAAGATGCAGCCGCACAAAGATATGCTGCGCAAGTCCTTC
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 14
--------------------------gtttgcatatgcatgatcaatctgttcttcttcttttttcgtttgtgactgagaaagattctgagattaattgatatgtatgaagGTCTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGC
| | | || | ||| | ||| | | |||| || | || | | | ||| ||| || | ||| | | || ||| ||| ||||||| ||||||||||| ||| |||| |||||||| || | ||||||||||| ||||| | ||| |||||||||||||||||||| | |
gttgcaatttttatgccattccaagggctcatttctgaaagat-gctttgtaccttatcttgttatgggcttgtc--atagtaattatgatatcatttgttttata----gGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttttttcgtttgtgactgagaaagattctgagattaattgatatgtatgaagGTCTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGC
attaattgatatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcatatgcatgatcaatctgttcttcttcttttttcgtttgtgactgagaaagattctgagattaattgatatgtatgaagGTCTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT