Sequence
atgc intronic sequence ATGC exonic sequencegtatgagtttgttatatatggattttcgatgagtctataccatagacttgtgatagttcacatgatacatattgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55930.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 6
-----------gtatgagtttgttatatatggat--tttcgatgag-tctataccatagacttgtgat------agttcac---atgatacatattgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
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gtattgtactattcagaatttctgatccatccctgcttgtactgaactcttagctagttattcttgatcagctaaattcaatgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 6
-------------gtatgagtttgttatatatggat-tttcgatgagtctataccat----agacttgtgatagtt------cacatgatacatattgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
| | || || | ||| ||| ||| || | | || | | || | | | || || | |||||||||||||||||||||||||||||||||||||| || || ||||| |||| || ||||| |||||||||||||| |||||||| |||| || |||||||
ttgcaaaagccttatcttcattgattgt-tatagatattttaatccatttttatttctgtcaaaatttaaacatctctcacacatatataatatattgcagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 6
-------------------------gtatgagtttgttatatatggattttcgatgagtctataccatagacttgtgatagttcacatgatacatattgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
| | | | || | | | | | | | | | | | | | | | || ||| ||||| |||||||||||||||||||||||||||||||| || || ||||| ||||||| ||||| |||||||||||||| |||||||| |||| || |||||||
cttatcttcattgattgttatagatattttaatccatttttatttgtctgttaaaatttaagcatctcaaatatatatatatatatat-ata-atattacagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
upper sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 6
---------------gtatgagttt-gttatatatggattttcgatgagtctatac-----catagacttgtgatagttcacatgatacatat--tgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
| | ||| | |||| | | |||| ||| || | | | || | | | ||| || | ||||||||||||| ||||||||||| |||||||| ||||| |||||| |||| |||||||| |||||||| ||||| |||||||| |||| ||| | | || |
ttattgacttaatgggcagaagtaaagctatacttagtttttggatctgtgtgtgtgtgtgtgtggataagatgctatcgctgtaataaatctcttgcagGATATGATCGAAAATGTGTTGGAGATAAAAGATACACATGTTAGAGAAGTGATGACACCTCTTGTGGATGTTGTTGCAATTGATGCCAGTGCAACACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcgatgagtctataccatagacttgtgatagttcacatgatacatattgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
atacatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagtttgttatatatggattttcgatgagtctataccatagacttgtgatagttcacatgatacatattgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC