Sequence
atgc intronic sequence ATGC exonic sequencegcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G49310.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 4
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
|| || ||| | | | | | | | | ||| || ||| | | | | || | | | || | | | | | | | ||||||||||||||||||||||| || ||||| ||||| || || || | || |||||||| ||||||||||| ||||| || ||| | |||||||| |||||
-----------------------------------gtagatttatca-tgtccaccatagcaa---agggcataatgtttttttaaatatttttttttattttaacatatcaa-atggtttcttttgaaatttcagATGAAAAGATTGCATTGCTTGGAGCTATACAGTCACTGTTTGAGGGTTCAATGTACACTTTTGTTTTCCTGTGGACTCCTGCTTTGAGCCCAAATGATGA
upper sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 4
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
| | || | || | | |||||| | | | | | | | ||||||| || | | | |||||||||||||||||||| ||||| || || ||||| | || || | |||||||||||| ||||| ||||| ||||| ||||| | |||||||| || ||
-------------------------------------gtatgctttagcccgtctcatcagaacgcagagaaccaaatatttatgcatatgaaacctgcatttgttt-tctaacatcgtccac--tggatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCGATGTACACATTTGTCTTCCTATGGACTCCAGCGTTGAGCCCAAATGAAGA
upper sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
| | || || | || | | | | || || || || || ||||| | |||||| | || || || | |||||||||||||||||||| ||||| || || ||||| | || || | ||| |||||||| ||||| ||||| ||||| ||||| | || ||||| || ||
--------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgcct-----tctaacgctgtccat--ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
upper sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
| | || || | || | | | | || || || || || ||||| | | |||| | || || || | |||||||||||||||||||| ||||| || || ||||| | || || | ||| |||||||| ||||| ||||| ||||| ||||| | || ||||| || ||
--------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgcct-----tgtaacgctgtccat--ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
upper sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttc---tcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
| | | | ||| | ||| || || ||| | | | | | ||| || | | ||| | | |||| || | |||||||| || || ||||||||||| || || ||||||||||| |||| || |||||||| ||||| ||||| ||||| || ||| | || || || || ||
-------------------------------------atatattttctttctttcttctttgatttattttata-tgcttggaagtttcttttttattttctttttattttaatattgt-tatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
upper sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 4
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
| || || | ||| || || || || |||| ||| ||||| || | || ||| | | || || || || | || | | || | |||||||| || ||||| |||||||| || |||||||| | || |||| ||| ||||| || ||||| ||||||||||| || ||||| |||||||| || ||
----------------cattg--tttgctatcccaatgggtttatccat-----ctgtttcc--tcatcttttc----agttttttcc------tcctttcttggagctttagtattatgtttcat-gtggttcagATGAGAAAATTGCGTTGCTGGGTGCAATTCAGTCGTTGTTTGAAGGCTCAATGTATACTTTTGTGTTCCTCTGGACTCCTGCTCTAAGCCCAAATGAAGA
upper sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------gca-ggttcaaagttagcgttaaaactgttgattcaaaaggctt----ctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtt-tcctcatctctctaacacaatctatgattatttct---cagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
|| ||| || | || | | || | || || || ||| | | || ||| ||| | || | | | | | | | | | | | | | | | | || || |||||||||||||||| | |||| ||||| || || | ||||||| || ||||| || ||||||||||||||||||||||| | || || | ||| |
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggac-gcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
ctctaac putative branch site (score: 2)
ttatttctc putative PPT
aatctatgattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC