Sequence
atgc intronic sequence ATGC exonic sequencegtgagtggagaaatctgtttttaaatagagtgatgtttgttttagcattgctgatttgtttggatggttgatttgatttgtaaccagGTGGTTGGGTTGGATACTTTTCATATGACACTGTACGTTATGTTGAGAAGAAGAAGCTGCCTTTTTCTAATGCTCCAGAGGATGATAGGAGTCTTCCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G29690.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G29690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g61120.1 (Oryza sativa), 3'ss of exon 3
---------------gtgagtggagaaatctgtttttaaatagagtgatgtttgttttagcattgctgatttgtttggatggttgatttgatttgtaac-cagGTGGTTGGGTTGGATACTTTTCATATGACACTGTACGTTATGTTGAGAAGAAGAAGCTGCCTTTTTCTAATGCTCCAGAGGATGATAGGAGTCTTCCTGA
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ttgttgtctttttctttcagctaacaaagtggtctt---gcaaatatattccctctaaagccatgataatttattctgttgcatcttgggatttattttacagGAGGATGGGTTGGATTCTTCTCTTACGACACAGTGCGTTATGTTGAAACAAAGAAGCTTCCATTTTCTAACGCGCCAGAGGATGATAGGAACCTTCCTGA
upper sequence: AT2G29690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g15780.2 (Oryza sativa), 3'ss of exon 2
gtgag-tggagaaatctgtttttaaataga--------gtgatgtttg-ttttagcattgctgatttgt----ttggatggttgattt---gatttgtaaccagGTGGTTGGGTTGGATACTTTTCATATGACACTGTACGTTATGTTGAGAAGAAGAAGCTGCCTTTTTCTAATGCTCCAGAGGATGATAGGAGTCTTCCTGA---------------------------------
||||| | |||||| || ||| | || |||| |||| | ||| ||| | ||| ||| ||||| | |||||| ||||| || | |||||| ||||| || || ||||||||||| |||||||||||||| || || |||||| |||| ||||||| ||||||||
gtgagctaacgaaatcaaacagtaggaagaagaaatggggaatatttgattttgttggttatgaaatgtgaaccatggcatttggtttctttgtttgtgat-aggtggatgggtcgggttcttttcctatgatacagTCCGTTATGTTGAAAAGAAGAAGCTGCCCTTCTCCGGTGCTCCCCAGGACGATAGGAACCTTCCTGATGTTCACCTTGGGCTTTATGATGATGTTCTCGT
upper sequence: AT2G29690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g15780.1 (Oryza sativa), 3'ss of exon 2
gtgag-tggagaaatctgtttttaaataga--------gtgatgtttg-ttttagcattgctgatttgt----ttggatggttgattt---gatttgtaaccagGTGGTTGGGTTGGATACTTTTCATATGACACTGTACGTTATGTTGAGAAGAAGAAGCTGCCTTTTTCTAATGCTCCAGAGGATGATAGGAGTCTTCCTGA
||||| | |||||| || ||| | || |||| |||| | ||| ||| | ||| ||| ||||| | |||||| ||||| || | |||||| ||||| || || ||||||||||| |||||||||||||| || || |||||| |||| ||||||| ||||||||
gtgagctaacgaaatcaaacagtaggaagaagaaatggggaatatttgattttgttggttatgaaatgtgaaccatggcatttggtttctttgtttgtgat-agGTGGATGGGTCGGGTTCTTTTCCTATGATACAGTCCGTTATGTTGAAAAGAAGAAGCTGCCCTTCTCCGGTGCTCCCCAGGACGATAGGAACCTTCCTGA
upper sequence: AT2G29690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 2
gtgagtggagaaatctgtttttaaatagagtgatgtttgttttagcattgctgatttgtttggatggttgattt-gat------ttgtaaccagGTGGTTGGGTTGGATACTTTTCATATGACACTGTACGTTATGTTGAGAAGAAGAAGCTGCCTTTTTCTAATGCTCCAGAGGATGATAGGAGTCTTCCTGA
||||| | || | || |||| || | || | || || || | || || || ||| | | || | |||||| |||||||| | |||||| ||||| || || | |||||||||||||||||||| || || || | |||||| |||| ||||||| ||||||||
gtgagcagcctcgattgctgagaaggagagaagatttgatgttgccgatgatg--ttatgtgaatagtcacttttggtcttctgttcttgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA
upper sequence: AT2G29690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S154_79V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------gtgagtggagaaatctgtttttaaatagagtgatgtttgttttagcatt-gctgatttgtttggatggttgatttgatt-tgtaaccagGTGGTTGGGTTGGATACTTTTCATATGACACTGTACGTTATGTTGAGAAGAAGAAGCTGCCTTTTTCTAATGCTCCAGAGGATGATAGGAGTCTTCCTGA
||||| | | |||| | | || | | | | ||||| ||||| | ||| | || | || || || |||| || |||||||| |||||||||||||||||||| | ||||| ||||| |||||| |||| |||||| || || ||||| | || | |||||
gattacataaacgctgagtcgtaacatctcctatataacat--ttgcacattcctaagcatgagctgaaatttttagttgatatcttcgagcatggttgcagGAGGATGGGTTGGGTACTTTTCATATGACACTGTGAGGTATGTGGAGAAAAAGAAGTTGCCCTTTTCTTCAGCACCTATAGATGACCGAGGTTTACCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtttgttttagcattgctgatttgtttggatggttgatttgatttgtaaccagGTGGTTGGGTTGGATACTTTTCATATGACACTGTACGTTATGTTGAGAAGAAGAAGCTGCCTTTTTCTAATGCTCCAGAGGATGATAGGAGTCTTCCTGA
atttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtggagaaatctgtttttaaatagagtgatgtttgttttagcattgctgatttgtttggatggttgatttgatttgtaaccagGTGGTTGGGTTGGATACTTTTCATATGACACTGTACGTTATGTTGAGAAGAAGAAGCTGCCTTTTTCTAATGCTCCAGAGGATGATAGGAGTCTTCCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG