Sequence
atgc intronic sequence ATGC exonic sequencegtagatcatgctgtgattgaccattgaaaccgtttttttttcaatgttagcatttggtatggttactaactttttgttctaaagGTGATGCTTTGAGGAAACTTGAGGAAAGAGGAATTGTCATACGTTTTGTGATTGGTCGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G25300.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G25300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G32180.1 (Glycine max), 3'ss of exon 4
gtagatcatgctg-tgattgaccattg---aaaccgtttttttttcaatgttagcatttggtat--ggttactaactttttgttct----------aaagGTGATGCTTTGAGGAAACTTGAGGAAAGAGGAATTGTCATACGTTTTGTGATTGGTCGAAG
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gatgggaatgtaaacacttgactattttgtagatggttatctttttggttcaattgtatattactaagtcactgacatcttatcttctcttttctggcagGTGATGCCTTGAAAAAACTTGAAGAAAGAGGAGTGGTCATACGTTTTGTTATTGGTCGGAG
upper sequence: AT2G25300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G14000.2 (Glycine max), 3'ss of exon 4
gtagatcatgctg-tgattgaccattg---aaaccgtttttttttcaatgtta--gcatttggtatggttactaactttttgttct----------aaagGTGATGCTTTGAGGAAACTTGAGGAAAGAGGAATTGTCATACGTTTTGTGATTGGTCGAAG
| || ||| ||||| ||| | | ||| | |||| | | | | || | | | || ||| || | || | | ||||||||| |||| |||||||| ||||||||| | |||||||||||||| |||||||| ||
gatgagaatgtaaacacttgactattttgtagatggttatctttttggtttaattgtatattgcctagtcactgacatcttatcttctcttttctggcagGTGATGCCTTGAAAAAACTTGAAGAAAGAGGAGTGGTCATACGTTTTGTTATTGGTCGGAG
upper sequence: AT2G25300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0008g06480.t01 (Vitis vinifera), 3'ss of exon 4
----------gtagat--catgctgtg---attgaccattgaaaccgtttttttt----tcaatgttagcatttggtatggttactaactttttgttctaaagGTGATGCTTTGAGGAAACTTGAGGAAAGAGGAATTGTCATACGTTTTGTGATTGGTCGAAG
||| | || |||| | || | || | | | | || | | | || | | || | | || | | | || ||||| | |||||||||||||||||| | ||||||||||| || |||||||| ||
gcttaattgcataggtttcagattgtgtgcagtggctatcaagaatctatgcattgagtttacaaacaatatatcatgtgaagtttcatggcttttgcagGTGAGGAAGCTTTAAAAAAACTTGAGGAAAGAGGAGTGGTCATACGTTTCGTAATTGGTCGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgtttttttttcaatgttagcatttggtatggttactaactttttgttctaaagGTGATGCTTTGAGGAAACTTGAGGAAAGAGGAATTGTCATACGTTTTGTGATTGGTCGAAG
tactaac putative branch site (score: 0)
ctttttgttct CT-rich tract
tttttttcaatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatcatgctgtgattgaccattgaaaccgtttttttttcaatgttagcatttggtatggttactaactttttgttctaaagGTGATGCTTTGAGGAAACTTGAGGAAAGAGGAATTGTCATACGTTTTGTGATTGGTCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA