Sequence
atgc intronic sequence ATGC exonic sequencegtaattatctgcttctttcataactctcagttctatgaacttgcttacgaaaaggagcccaatatatttcacacatttaacttctccgattacctaatccaatggtagtatattcctctgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18510.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 3'ss of exon 7
gtaattatctgcttctttcataactctcagttctatgaacttgcttacgaaaaggagcccaatatatttcacacatttaacttctccgattacctaatccaatggtagtatattcctc-tgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG
|| | | || |||| | | | || | |||| | | | || | || | | || | | | || ||| |||||| ||| |||| |||| || | ||| || |||||||| || |||||||||||||| |||||||| |||||||| || || ||||
----------------------------------------------------------gtaacacaattgccacaataagttctatattttgtttcttccatttattgaatgtgtttcaccttatgtgccacaattttccagGCAATGAACAACCAACATCTATGTAACCGGCCAATTACTGTCTCTTATGCCTACAAGAAAGACACAAAAGGAGAACGCCATGGCACACCTGCAG
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 7
gtaattatctgcttctttcataactctcagttctatgaacttgcttacgaaaaggagcccaatatatttcacacatttaacttctccgattacctaatccaatggtagtatattcctctgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG
||| | | || || || | | | || | ||| | | || || | || || | || | || || ||| | || ||| | |||| ||| || | | || || | |||||| |||||||| || |||||||||||||| ||||||||||||||||| || |||||||
------------------------------cactacaatcc-----acatggagtggcactacaaggaacaggcccttagtgattttggttgtctggctt--ttgtttcatgcttcttt---ctgtg-ctgtatttttcagGCCATGAACAACCAACATTTGTGCAACCGGCCAATCACTGTCTCTTATGCTTACAAGAAAGACACAAAAGGAGAGCGCCATGGCACACCAGCAG
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 5
gtaattatctgcttctttcataactctcagttctatgaacttgcttacgaaaaggagcccaatatatttcacacatttaacttctccgattacctaatccaatggtagtatattcct-ctgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG
|| | | | || | ||||| |||| | || | | ||| ||| | | ||| | ||| | | | | | || ||| | |||| ||| || | | || || | |||||| |||||||| || |||||||||||||| |||||||| |||||||| || |||||||
--------------------------------------------gtaatggagtcatcacactg-atttcctgtatttcaatttgcagtggttctagctgtctggcatttgtttcatgctgctttctctgctatattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 7
gtaattatctgcttctttcataactctcagttctatgaacttgcttacgaaaaggagcccaatatatttcacacatttaacttctccgattacctaatccaatggtagtatattcctctgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG
| | ||| || | | || | | ||| | |||| | | || || ||| | ||| || || | ||| ||| ||||| || |||||| |||||||||||| | ||||||||||| ||||| || || || || ||||||||||| || || || || |||||||| |||||||
--------------------tctgtttcaattttgttgtctgggtattcaaatcattcgtaatag---tagaatataaaagcattcccacg-------ccactgatattgaatttttctatattttgt-----------agGCAATGAATGGACAATATCTTTGCAATCGTCAAATTACAGTGTCATATGCTTATAAGAAAGACACTAAGGGTGAACGGCATGGTACCCCAGCAG
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 7
gtaattatctgcttctttcataactctcagttctatgaacttgcttacgaaaaggagcccaatatatttcacacatttaacttctccgattacctaatccaatggtagtatattcctctgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG
||| | || | | ||| | || | | | | | | ||| | |||| ||| | | | || | || || || | ||| ||| ||||| || |||||| |||||||||||| | ||||||||||| ||||| || || || |||||||||||||| || || || || |||||||| || || |
-------------tctgtttcaatttt--gttgtctggatatccaaatcatacggaac--aatagattataaaagcat----tcccacgccacata---------tattgaatttttctatattttgt-----------agGCAATGAATGGACAATATCTTTGCAATCGTCAAATTACAGTGTCATATGCTTACAAGAAAGACACTAAGGGGGAACGGCATGGTACCCCGGCTG
upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 7
gtaattatctgcttctttcataactctcagttctatgaacttgcttacgaaaaggagcccaatatatttcacacatttaacttctccgattacctaatccaatggtagtatattcctctgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG
| | | | ||| | || || | || | | | | | | | | ||| | |||| || | |||||| |||||| ||| || |||||| | || || || || || || || || ||||||||||||||||| ||||| ||||| |||||||| |||||||
---------------------------------------cattatggcatcaagtcactcacc-catatgacttgatccatcttttattctgattgaattggagttagatttaggtgttgatgaccttcc-atatttgcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCATACAAGAAAGACACTAAAGGGGAGCGGCATGGTACCCCAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgattacctaatccaatggtagtatattcctctgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG
gtctgac putative branch site (score: 3)
tagtatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattatctgcttctttcataactctcagttctatgaacttgcttacgaaaaggagcccaatatatttcacacatttaacttctccgattacctaatccaatggtagtatattcctctgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA