Sequence
atgc intronic sequence ATGC exonic sequencegtatttcatcatgatatgataattagtctcttaccatattcaattgtctctgcttaaaggctgacaagggaaaacttatactcttgcagTATGCAGCGAAACTTCTAAAGAAACCTGATCAATGTCGAGCTGTTTATGCCTGTTCTCATTTGTTCTGGCTGGAAGATCGTGAGACCATACAAGATGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G17790.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 19
-----------------------gtatttcatcatgatatgataattagtctcttaccatat-----tcaatt--gtctctgcttaaaggctgacaagggaaaactta-tactcttgcagTATGCAGCGAAACTTCTAAAGAAACCTGATCAATGTCGAGCTGTTTATGCCTGTTCTCATTTGTTCTGGCTGGAAGATCGTGAGACCATACAAGATGGAG
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gtaacaattactatgctgtttccttattgaattatgtttttctcttctctctctctctctctctctctcaaatcagtctcttctatgcacataataacatcctgctgaataattgtgcagTACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCATGTTCACACCTTTTCTGGACTGACGACCAAGACGGAATAATGGATGGTG
upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
----------------gtatttcatcatgatatgataattagtct--cttaccatattcaattgtctctgcttaaaggctgacaagggaaaacttatactcttgcagTATGCAGCGAAACTTCTAAAGAAACCTGATCAATGTCGAGCTGTTTATGCCTGTTCTCATTTGTTCTGGCTGGAAGATCGTGAGACCATACAAGATGGAG
| | || ||| ||| ||||| || | | | |||||| | || | ||| | | || || ||||||| |||| |||||||| ||||| ||||||||||| ||||| |||||||| ||||| ||| | |||||| || || | || ||| ||||| |
cttaatgtagcctctcgagaactgttattgcatgg-aatcagtcttctttggaccaagcgctagtctcttttgtaaa--ttacattgctattgtttta----tgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM5G844195_T04 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------gtat-ttcatcatgatatgataatt------agtctcttaccatat---tcaattgtctctgcttaaag-gctgaca--------agggaaaacttatact----cttgcagTATGCAGCGAAACTTCTAAAGAAACCTGATCAATGTCGAGCTGTTTATGCCTGTTCTCATTTGTTCTGGCTGGAAGATCGTGAGACCATACAAGATGGAG
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gtaatgattcttgttttatggctagttcatttccccctcaatccccccttcaatccccatggggaatgggtgtatccaaagtagccttgtagcctcgcgagacctgttattgcatgaatcagctttctttaaatgaagtgctagcctctcttgtaaattacattgctactgctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catattcaattgtctctgcttaaaggctgacaagggaaaacttatactcttgcagTATGCAGCGAAACTTCTAAAGAAACCTGATCAATGTCGAGCTGTTTATGCCTGTTCTCATTTGTTCTGGCTGGAAGATCGTGAGACCATACAAGATGGAG
ggctgac putative branch site (score: 3)
tactctt putative PPT
aaaacttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcatcatgatatgataattagtctcttaccatattcaattgtctctgcttaaaggctgacaagggaaaacttatactcttgcagTATGCAGCGAAACTTCTAAAGAAACCTGATCAATGTCGAGCTGTTTATGCCTGTTCTCATTTGTTCTGGCTGGAAGATCGTGAGACCATACAAGATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA