Sequence
atgc intronic sequence ATGC exonic sequence...aatttgactgcagactaaatttcgttgctattttgttcctatggtagatgctatctaaaattatcttgaagtcgtatttggaggcttaaccactgtatagATACACTACAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATTTCCAGGAGGTTCAGAATTTGATATCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G35980.2 |
intron # | 8 |
splice site | 3' |
intron type | U12 (go to U12 genes for details) |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G35980.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G156638_T02 (Zea mays), 3'ss of exon 5
-aatttgactgcagactaaatttcgttgctattttgttcctatggtagatgctatctaaaattatcttgaagtcgtatttggaggcttaaccactgtatagATACACTACAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATTTCCAGGAGGTTCAGAATTTGATATCTTG
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ttacttacgtgtatttttcaataaagtgctgccattctgctgttctgg-cattttcttagatgcaattgaagtagccttcttgaaccttaacatttaatagATATACTACCGCGATCGACATGTGGTCGTTTGGCTGCATAGTTGCTGAACTGTTTCTAGGTTTGCCATTGTTTCCTGGAGCGTCAGAATATGATGTGCTT
upper sequence: AT5G35980.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G18110.1 (Glycine max), 3'ss of exon 10
-----aatttgactgcagactaaatttcgttgctattttgttcctatggtagatgctatctaaaattatcttgaagtcgtatttggaggcttaaccactgtatagATACACTACAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATTTCCAGGAGGTTCAGAATTTGATATCTTG
| | | | | ||| | ||||||| | | || ||| || || | | | |||| |||||| | | |||||||| ||||||||||| |||||||| ||||| ||||| || || || ||||||||||||| ||| |||| || || | ||||||||||||| | |||
tgtttcacattcttaatgcgtgtattcttcagaagttttgtttcctttttaa----tatttatttttgtgtacttgcttcattttagtccttaactcttat-cagATACACAACAGCTATTGATATGTGGTCCTTTGGGTGCATAGTGGCGGAATTGTTTCTTGGATTACCATTATTCCCCGGGGCTTCAGAATTTGATCTTTTG
upper sequence: AT5G35980.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv16s0039g00610.t01 (Vitis vinifera), 3'ss of exon 7
aatttgactgcagactaaatttcg-ttgctattttgttcctatggtagatgctatctaaaattatcttgaagtcgtatttggaggcttaaccactgtatagATACACTACAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATTTCCAGGAGGTTCAGAATTTGATATCTTG
||||| |||| |||||| | || ||| || | | | | | | || | || || | || | ||||||| | | || || ||||| ||||||||||||||||||||||| || || ||||| ||| ||||||| || ||||| |||||||| |||| ||||||||||||| | |
tgtttga-tgcatttgaaattttaatcatgatagggtttctgtactcaaatttgttcatgggtaacatggtgtttcagtttggaccttaacccttttccagGTATACTACGGCTATTGACATGTGGTCTTTTGGGTGTATAGTTGCTGAGTTGTTTCTAGGGTTGCCGCTATTTCCCGGAGCTTCAGAATTTGATCTTCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatgctatctaaaattatcttgaagtcgtatttggaggcttaaccactgtatagATACACTACAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATTTCCAGGAGGTTCAGAATTTGATATCTTG
aggcttaac putative branch site
tatctaaaattatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttgactgcagactaaatttcgttgctattttgttcctatggtagatgctatctaaaattatcttgaagtcgtatttggaggcttaaccactgtatagATACACTACAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATTTCCAGGAGGTTCAGAATTTGATATCTTG
- - - - - - gactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - atctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatttgg