Sequence
atgc intronic sequence ATGC exonic sequencegttggtaaccactccttgtgcataagttatgaaatacacctttggtctgtaacgagcatttgacctgtgaaatttaggcttagccttcgaaacgtcaaatatacgctttgatttctttgctgacgcatgaaagtttttcccaaattacaatagGTTGCTAAAGTATTGGTTGAAGTGTTTGCTGAAATGATATTTGTTCACGGGTTCATACATGGCGATCCGCATCCTGGAAATATACTAGTTTCTCCTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65950.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os11g34750.1 (Oryza sativa), 3'ss of exon 11
gttggtaaccactccttgtgcataagttatgaaatacacctttggtctgtaacgagcatttgacctgtgaaatttaggcttagccttcgaaacgtcaaatatacgctttgatttctttgctgacgcatgaaagtttttcccaaattacaat-agGTTGCTAAAGTATTGGTTGAAGTGTTTGCTGAAATGATATTTGTTCACGGGTTCATACATGGCGATCCGCATCCTGGAAATATACTAGTTTCTCCTGAAG
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---------------------------------------------------attctaattttgcttgttatacttgatattaaaattttattcactgacta-gctaattgatttttct-ctgtttt-tggtacctttctatgcttatcattcagGTAGCTAAAGCATTAATTGAACTGTTTGGCGAAATGATTTTTGTACATGGTTTTGTTCATGGCGATCCTCATCCTGGAAATATATTAGTTTCTCCTCAAG
upper sequence: AT1G65950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os11g34830.1 (Oryza sativa), 3'ss of exon 8
gttggtaaccactccttgtgcataagttatgaaatacacctttggtctgtaacgagcatttgacctgtgaaatttaggcttagccttcgaaacgtcaaatatacgctttgatttctttgctgacgcatgaaagtttttcccaaattacaatagGTTGCTAAAGTATTGGTTGAAGTGTTTGCTGAAATGATATTTGTTCACGGGTTCATACATGGCGATCCGCATCCTGGAAATATACTAGTTTCTCCTGAAG
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---------------------------------------------------attctaattttgcttgttatacttgatattaaaattttattcactgacta-gctaattgatttttct-ctgtttttggtacctttctatgcttatcttttagGTAGCTGAAACATTAATTGAATTGTTTGGCGAAATGATTTTTGTACATGGTTTTGTTCATGGCGATCCTCATCCTGGAAATATATTAGTTTCTCCTCAAG
upper sequence: AT1G65950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G040720_T01 (Zea mays), 3'ss of exon 8
gttggtaaccactccttgtgcataagttatgaaatacacctttggtctgtaacgagcatttgacctgtgaaatttaggcttagccttcgaaac---gtcaaatatacgctttgatttctttgctgacgcatgaaagtttttcccaaattacaatagGTTGCTAAAGTATTGGTTGAAGTGTTTGCTGAAATGATATTTGTTCACGGGTTCATACATGGCGATCCGCATCCTGGAAATATACTAGTTTCTCCTGAAG
|||||| | | | || | || | || | ||| | | |||| | | | ||| | | || | | |||| ||||| | ||| ||||| | |||| ||||||||||||||| || || || | || || ||||| ||||||||||||||| |||||||||||||||
-----------------------------------------------------atgcattt---ttttatatttcatcatttgtttttgtaacttaatttcaactacgtctctttgtacttggtacaaaaaaaacacctgcttttgtatcttccagGTAGCTAAGGCTTTGATTGAACTCTTTGGTGAAATGATATTTGTACATGGTTTTGTTCACGGTGATCCACATCCTGGAAATATATTAGTTTCTCCTGAAG
upper sequence: AT1G65950.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G40830.1 (Glycine max), 3'ss of exon 9
gttggtaaccactccttgtgcataagttatgaaatacacctttggtctgtaacgagcatttgacctgtgaaatttaggcttagccttcgaaacgtcaaatatacgctttgatttctttgctgacgcatgaaagtttttcccaaattacaatagGTTGCTAAAGTATTGGTTGAAGTGTTTGCTGAAATGATATTTGTTCACGGGTTCATACATGGCGATCCGCATCCTGGAAATATACTAGTTTCTCCTGAAG
| | | || | | | | | | | ||| | | | | | | | | || | ||| ||| |||| ||| | | |||| |||| || ||| |||| ||| |||||||||||||||||||||| || || | ||||||||| ||||| || ||||| |||||| |||||||||||||||
---------------------------------------atcagatgaatatcaa-ctctaatctcattcatttt--gttcaactgttgtagtgctaagtgctaacttg-----cttaactgattcattttaaaact------gttactgaagGTAGCAAAATCATTGACTGAGCTGTTTGCTGAAATGATATTTGTACATGGCTACATACATGGTGATCCACACCCTGGTAATATATTAGTTTCTCCTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatacgctttgatttctttgctgacgcatgaaagtttttcccaaattacaatagGTTGCTAAAGTATTGGTTGAAGTGTTTGCTGAAATGATATTTGTTCACGGGTTCATACATGGCGATCCGCATCCTGGAAATATACTAGTTTCTCCTGAAG
tgctgac putative branch site (score: 2)
aaattacaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtaaccactccttgtgcataagttatgaaatacacctttggtctgtaacgagcatttgacctgtgaaatttaggcttagccttcgaaacgtcaaatatacgctttgatttctttgctgacgcatgaaagtttttcccaaattacaatagGTTGCTAAAGTATTGGTTGAAGTGTTTGCTGAAATGATATTTGTTCACGGGTTCATACATGGCGATCCGCATCCTGGAAATATACTAGTTTCTCCTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG