Sequence
atgc intronic sequence ATGC exonic sequencegtacattttgagtaactatgagtagaaatggagagttagtttacctatctagttgtccctgtacttgttaagtaacctcttcggatttatgtctacagCCCAACACGGCCCAACCCAGGAGGTGGAGGAGAAACTTGTGCAGAAACTGGAATCAATATTTTCTTCACAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12280.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA04G36700.1 (Glycine max), 3'ss of exon 12
-----------gtacattttgagtaactatgagtagaaatggagagttagtttacctatctagttg--tccctgtacttgttaagtaacct-cttcggatttatgtcta----cagCCCAACACGGCCCAACCCAGGAGGTGGAGGAGAAACTTGTGCAGAAACTGGAATCAATATTTTCTTCACAAAG
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gtataacaaggatgctctggaagtatctatatatgtaaattttca-ttatttcaatt-tttagccactttactgttttgttttggtgctttgttttgaatgtttgtccaatgccagCCCAACAAAGCCCAATCCAGGAGGTGGAGGGGAAACATGTGCAGAAACTGGGATCAACATTTTTTTTGGCAAG
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G26170.1 (Glycine max), 3'ss of exon 11
---------gtacattttg--agtaactatgagtagaaatggagagttagtttacctatctagttg--tccctgtacttgttaagtaacct-cttcggatttatgtcta---cagCCCAACACGGCCCAACCCAGGAGGTGGAGGAGAAACTTGTGCAGAAACTGGAATCAATATTTTCTTCACAAAG
| | | || |||| |||| | |||| |||| || | | | ||| | |||| | || || | || | || | | || | |||||||||| ||| || |||||||||||||| ||||| |||||||||||||| ||||| ||||| || |||
gtataacaaggatgatctggaagtatctatatatgtaaattttc-gttatttcaatt-tttagccactttactgttttcttttggtgctttgttttgaatgtttatccaatgcagCCCAACAAAGCCAAATCCAGGAGGTGGAGGGGAAACATGTGCAGAAACTGGGATCAACATTTTTTTTGGCAAG
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G36890.1 (Glycine max), 3'ss of exon 11
---------gtacattttg--agtaactatgagtagaaatg---gagagttagtttacctatctagttgtccctgtacttgttaagtaacctc--ttcggatttatgtc---tacagCCCAACACGGCCCAACCCAGGAGGTGGAGGAGAAACTTGTGCAGAAACTGGAATCAATATTTTCTTCACAAAG
| | | || |||| ||| | |||| | ||| || | | || ||| || || | | | || | || | ||| | |||||| ||| ||| || |||||||||||||| ||||| |||||||||||||| ||||| || || || |||
gtataacaagaatgatctggtagtacttatatatgtaaattttcattatttaaatttttaaccactttactgttgtttttcttttggtgctttgttttgaatgtttgttcaatgcagCCCCACAAAGCCAAATCCAGGAGGTGGAGGGGAAACATGTGCAGAAACTGGGATCAACATCTTTTTTGGCAAG
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv04s0008g02780.t01 (Vitis vinifera), 3'ss of exon 11
gtacattttgagta-actatgag----tagaaatggagagtt-agtttacctatctagtt-gtccctgtacttg-ttaagtaacctcttcggatttatgtctacagCCCAACACGGCCCAACCCAGGAGGTGGAGGAGAAACTTGTGCAGAAACTGGAATCAATATTTTCTTCACAAAG
|||| |||| ||| ||||| || || |||| | | | | | | | || || | | | | || | || | |||| | ||| ||| ||||||||||| || |||||| | | ||| ||||| |||||||||||||| |||||||| ||||| | |||
gtactgtttgggtacactataaggttttaaaaattgcaaatccaatccatgttactgcttcatattttcatctaatttggagttcttcttggatattcatctgcagTCCAACACGGCCAAATCCAGGACGCGAAGGGGAAACATGTGCAGAAACTGGCATCAATATATTCTTTAGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctatctagttgtccctgtacttgttaagtaacctcttcggatttatgtctacagCCCAACACGGCCCAACCCAGGAGGTGGAGGAGAAACTTGTGCAGAAACTGGAATCAATATTTTCTTCACAAAG
aagtaac putative branch site (score: 2)
ttaagtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacattttgagtaactatgagtagaaatggagagttagtttacctatctagttgtccctgtacttgttaagtaacctcttcggatttatgtctacagCCCAACACGGCCCAACCCAGGAGGTGGAGGAGAAACTTGTGCAGAAACTGGAATCAATATTTTCTTCACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA