Sequence
atgc intronic sequence ATGC exonic sequencegttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaaatgttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G14940.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 2
gttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaaa--tgttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAG
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gttagtcggcgaaacagc-gcgatttgctcacaccacatga--tgtagtttctagtctctaatctcgattgtaacattcttatttcagGATTCGGAACTGTCTGGTTCAGCTTTATTCAAAGGATATCACTCCAGATGACAAGCAAGAGCTTGATGAGGCTCTCCAGAGAGAG
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 2
gttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaaatgttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAG
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gttagtttgccaaccagt-gcattgtagttgacatgc-acaacttcgttca---gcctttaatcttgatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAG
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
gttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaaatgttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAG---------------
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gttagtttgccaaccagt-gcattgtagttgacatgc-acaacttcgttca---gcctttaatcttgatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 2
------------------gttagtttttgacttagttgttttctggagagagtgagaaaactc---tgttt-------gcttgtgt-gttgacctgacattaaatgttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAG
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gtttgttctccagttaccgtaatatttttattc--ttgtaaacgtaagagagggaaaagggttatttgcttcacataggctcttgttgatgctttgtttttccttcccttttcagGATAAGGAATTGCTTGGCCCAGTTATATGCTAAGGACATCACTCCTGATGATAAGCAAGAGCTTGATGAGGCTTTACAAAGAGAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86073317|gb|DR369074.1|DR369074EST: GCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAG GATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGA
genomic: GCTCATCCTACTCAGTCTGTGCGTAGATCATTGCTTCAGAAGCATGGGAGgttagttttt ... gttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtgagaaaactctgtttgcttgtgtgttgacctgacattaaatgttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAG
acctgac putative branch site (score: 3)
tgttttctc putative PPT
acattaaatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaaatgttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA