Sequence
atgc intronic sequence ATGC exonic sequencegtctgtgacatatttttgttcctctcttagtttcatagctgagtgattttgatatgtatgataatttgtattatataatgctgttggtatatgcatctttagGTATACAAGGGAGGATTGTTTAAAACTGCAACTGAGCATAAAGAACAAATCCGCTACTTCAGCCAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63950.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63950.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G00400.1 (Glycine max), 3'ss of exon 16
-----gtctgtgacatatttttgttcctctcttagtttcatagctgagtgat-tttgatatgtatgataatttgtattatata-atgctgttggtatatgcatctttagGTATACAAGGGAGGATTGTTTAAAACTGCAACTGAGCATAAAGAACAAATCCGCTACTTCAGCCAGCAG
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tgggtatgtatgtcatagttttgat------tgaactacatgggcaaaaaatatgcgatttagacattgattggctttttttacactcaaattgcatat---tttatagGTATACAAGGGAGGATTATTCAAAACTGCTACTGAACATAAAGAACAAATTCGGTACTTTAGCCAGCAG
upper sequence: AT5G63950.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA05G32740.1 (Glycine max), 3'ss of exon 14
-gtctgtgacatatttttgttcctctcttagtttcatagctgagtgattttgatatgtatgataatttgtattatataatgctgttggtatatgcatctttagGTATACAAGGGAGGATTGTTTAAAACTGCAACTGAGCATAAAGAACAAATCCGCTACTTCAGCCAGCAG
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tgggtatg-tatgttatagttttgatagaactacaagggcaaaaaatatgcgctttagacattgattggcttttt-taacactcaaattgcatgt-tttatagGTATACAAGGGAGGATTATTCAAAATTGCTACTGAACATAAAGAACAAATTCGGTACTTTAGCCAGCAG
upper sequence: AT5G63950.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv04s0044g01680.t01 (Vitis vinifera), 3'ss of exon 15
-gtctgtgacatatttttgttcctctcttagtttcatagctgagtgattttgata--tgtatgataatttgtattatataatgctgttggtatatgcatctttagGTATACAAGGGAGGATTGTTTAAAACTGCAACTGAGCATAAAGAACAAATCCGCTACTTCAGCCAGCAG
| | || | | || | || |||||| | ||| || ||||| || | | | |||| | |||| | | || ||||| ||| |||||| |||||||||| |||||||||||| || |||||||||| || ||||||||||| |||
tattattatgatgataattttttaatatttgtttcaattatcctctattacaatgagtgtatcatggtat-tgttatg-attgctcaaaatgtgtga---tttagATATTCAAGGGGGGATTGTTTAGAACTGCAACTGAACACAAAGAACAAACTCGGTACTTCAGCCAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatatgtatgataatttgtattatataatgctgttggtatatgcatctttagGTATACAAGGGAGGATTGTTTAAAACTGCAACTGAGCATAAAGAACAAATCCGCTACTTCAGCCAGCAG
ttttgat putative branch site (score: 4)
catcttt putative PPT
tatgtatgataatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtgacatatttttgttcctctcttagtttcatagctgagtgattttgatatgtatgataatttgtattatataatgctgttggtatatgcatctttagGTATACAAGGGAGGATTGTTTAAAACTGCAACTGAGCATAAAGAACAAATCCGCTACTTCAGCCAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC