Sequence
atgc intronic sequence ATGC exonic sequence...ttacttgatacaatcattacccacattttagactagtttctagaatggcactttacaaaacttccttcgttcactcattagcataaatggaaaatttcagGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31750.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------ttacttgatacaatcattacccacatttta-gactagtttctagaatggcactttacaaaacttccttcgttcactcattagcataaatggaaaatttcagGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG
| | || | || | || || ||| | || ||| || |||| | |||| || | || || || || | |||||||| || || |||||||||||||| ||||| ||||| |||||||| ||||||||||| || | ||||||
gtcctcaagtttcttccaatctcaaattcataattcatgcagctcataaagaaagtatatgcatagaggccatgaacgatttcaggatacgaccatattacgttatgtactgttgcaaatcgaaattcga-catttatctgcttatttgatctgta-cagGAGGAGGTGGTCGACAGCTCTCTCGAGTTCCTCATCCTTGCTAGTGATGGCCTCTGGGACGTGGTGACCAACGAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 6
ttacttgatacaatca-ttacccacattttagactagtt----tctagaatggcactttacaaa-acttccttcgttcactcattagcataaatggaaaatttcagGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG
|| | || | | || | || ||| || | | || | | | || ||||| | | | ||||| | || || | ||| || |||||||| ||||| |||||||||||| |||||||||||||||||||| || ||||| || ||| | || |||
-taatatatgttgttaattttttaggcttcagaataatcatcctttatattcacctttcacaaatgatgaccttgttcagtaat--gcttttgtgggtcat---agGAGGAAGTTATTGATCACTCTCTCGAGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G056572_T03 (Zea mays), 3'ss of exon 6
ttacttgatacaatcattacccacattttag-actagtttctagaatggca--ctttacaaaacttccttcgttcact-cattagcataaatggaaaatttcagGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG
||| ||| | | | || || | || | | | || ||| ||| || | ||| | | |||| ||| || |||||||| |||||| | | ||||||||||| || |||||||||||||| || ||||| || || |||||||||
ttaattgttttttttgaaattttgatgaaagcagcagcagcagtattaatgatctgtactaaaattgacttgttgattacatt----taatcttgtgat---aggagGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 6
ttacttgatacaatcattacccacattttagactagtttctagaatggcactttacaaaacttccttcgttcactcattagcataaatggaaaatttc---agGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG
| || || | || | ||| | || | | | | | | | | || ||| || || || || || |||||||| |||||| | | ||||||||||| || |||||||||||||| || ||||| || || |||||||||
-catttaat-tgttttttttgaaattttgatgaaagcagcagcagcagtattaatgatctgtactaaaattgacttgttgat-tacatttaatcttgtgatagGAGGAAGTTGTTGATGACACACTCGAGTTTCTTATCCTTGCAAGTGATGGGCTGTGGGATGTGGTCTCTAACGAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 7
ttacttgatacaatcattacccacattttagactagtttctagaatggcactttacaaaacttcct---tcgttcactcat-tagcataaatggaaaatttcagGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG
| |||| || || | ||| || | || ||| | ||| | ||| | | || | | | | |||| || | || ||||| ||||||||||| ||||| || |||||||| ||||| || ||||| || || ||||| ||||| ||||| |||
ctgactgatcttctctatattcttatt---gatgtgccctta-aatcttatttttcttttctttttcatttgtatatttaagttgcatgtttgccattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 7
ttactt--gataca-atcattacccacattttagactagtttctagaatggcactttacaaaacttcc-ttcgttcactcattagcataaatg-gaaaatttcagGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG
| ||| ||| | ||||| | || | || | | | | | | || || | | || | | | | |||| | ||||||| ||||||||||| |||| ||||| ||||||||||| || ||||| |||||||| || ||||| ||||| | || |||
-tgctttagatttatgtcattctttgccttctccctccattccaaaa----ctttctgcagaatcagcactaattaatttactggcatttttctgaaaattgcagGAGGAAAAGATTGACAGCTCCCTCGAGTTTCTTATCCTTGCCAGTGATGGACTGTGGGATGTTGTCACAAATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggcactttacaaaacttccttcgttcactcattagcataaatggaaaatttcagGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG
ataaatggaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttacttgatacaatcattacccacattttagactagtttctagaatggcactttacaaaacttccttcgttcactcattagcataaatggaaaatttcagGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG
- - - - -acaatca
- - - - - - - - - acccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -tacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcataaa