Sequence
atgc intronic sequence ATGC exonic sequence...tgtcgcttcactttctactttttttttagttcaacttgaaccttaccagttttacttcaggtgtgaaagtaagttttaatctcctaattatttcatatagGTGGGAAAAAATCTACTGGGGGAAACTGGCTTTCAGTAAGTCAGGGAATAGCAGAGGACGCATCTGATCTTGTTTCGGGTTTTGCTACTATTGGTGATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73460.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 1
tgtcgcttcactttctactttttttttagttcaacttgaaccttaccagttttac---ttcaggtgtg--aaagtaagttttaatctcctaattatttcatatagGTGGGAAAAAATCTACTGGGGGAAACTGGCTTTCAGTAAGTCAGGGAATAGCAGAGGACGCATCTGATCTTGTTTCGGGTTTTGCTACTATTGGTGATGG
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-----tttctgattttggaatctgattgcccatacttattttttgctggagacacttgtttggatgtgctgaagactgtatttgactttttcatatatgcttcagGTATGAGGAGGGCTACAGGGGGCAGTTGGTTATCTGTAAGTCAAGGGATAGCAGAGGATACATCTGATCTTGTATCAGGATTTGCTACAGTTGGTGATGG
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 1
---tgtcgcttcactttctactttttttttagttcaacttgaaccttaccagttttacttcaggtgtgaaagtaagttttaatctcctaattatttcatatagGTGGGAAAAAATCTACTGGGGGAAACTGGCTTTCAGTAAGTCAGGGAATAGCAGAGGACGCATCTGATCTTGTTTCGGGTTTTGCTACTATTGGTGATGG
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ccatgacattaaggcctttgcttcaattcttttcccgctagaactaacataaactatttgtgcatattgaa-tgattttgactttttcatatatgt--ttcagGTGTGAGGAAGGCTGTAGGGGGCAGTTGGCTGTCTGTAAGTCAAGGGATTGCAGAGGATACATCTGATCTTGTATCAGGTTTTGCAACAATTGGGGATGG
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 6
tgtcgcttcactttctactttttttttagttcaacttgaaccttaccagttttacttc---aggtgtgaa-agtaagttttaatctcctaattatttcatatagGTGGGAAAAAATCTACTGGGGGAAACTGGCTTTCAGTAAGTCAGGGAATAGCAGAGGACGCATCTGATCTTGTTTCGGGTTTTGCTACTATTGGTGATGG
| | |||| | | | ||| | ||| | | || | ||| || | || || | | || ||| ||| ||| || | |||||| ||| | | ||||||| | ||||| || |||||||| || || |||||||| | |||||||| ||||| |||||||||||| ||||||| ||
-gatgtttca-tgtgttttttatgccctgttatgcatctttctgagagatttccttttgtaaaccgtaaagaatgagccttattcttgaaatgat--gactcagGTGGAAAACGAACAGCTGGGGGCAGTTGGCTATCTGTAAGTCAAGGCATTGCAGAGGATACCTCTGATCTGGTTTCTGGTTTTGCTACTGTTGGTGACGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagttttacttcaggtgtgaaagtaagttttaatctcctaattatttcatatagGTGGGAAAAAATCTACTGGGGGAAACTGGCTTTCAGTAAGTCAGGGAATAGCAGAGGACGCATCTGATCTTGTTTCGGGTTTTGCTACTATTGGTGATGG
tcctaat putative branch site (score: 2)
ttatttc CT-rich tract
taattatttcatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcgcttcactttctactttttttttagttcaacttgaaccttaccagttttacttcaggtgtgaaagtaagttttaatctcctaattatttcatatagGTGGGAAAAAATCTACTGGGGGAAACTGGCTTTCAGTAAGTCAGGGAATAGCAGAGGACGCATCTGATCTTGTTTCGGGTTTTGCTACTATTGGTGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - aacctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagtaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctaa