Sequence
atgc intronic sequence ATGC exonic sequence...ttagatttatttatggcccccgaggagccgtatgaggccaagacctcatgtacggttctgaaatagcggtgaaaatagtaatgttctcgccgactaggatTATCTAACAGTTTAAGTACAGTTGATATAGTTGAGGCACAATCAAAATATGGTTTTTGGGGATGGAATTTGTGGCGTCAACCTATAGGTTTTATCATTTT
Basic information
species | Arabidopsis thaliana |
transcript | ATCG01100.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: ATCG01100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Osp1g00960.1 (Oryza sativa), 3'ss of exon 1
ttagatttatttatggcccccgaggagccgtatgaggccaagacctcatgtacggttctgaaatagcggtgaaaatagtaatgttctcgccgactaggatTATCTAACAGTTTAAGTACAGTTGATATAGTTGAGGCACAATCAAAATATGGTTTTTGGGGATGGAATTTGTGGCGTCAACCTATAGGTTTTATCATTTT
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ctttccttttttctgatcatagaggagccgtatgaaactaaggtttcatgtacggttttggaatagcggtgggaactgtgatgttatcgtcgactatgatTATCCAACAGTTCAAGTACAGTTGATATAGTTGAAGCACAGTCAAAATATGGTTTTTTTGGATGGAATCTTTGGCGTCAGCCTATAGGTTTTCTGGTTTT
upper sequence: ATCG01100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G874448_T01 (Zea mays), 3'ss of exon 1
ttagatttatttatggcccccgaggagccgtatgaggccaagacctcatgtacggttctgaaatagcggtgaaaatagtaatgttctcgccgactaggatTATCTAACAGTTTAAGTACAGTTGATATAGTTGAGGCACAATCAAAATATGGTTTTTGGGGATGGAATTTGTGGCGTCAACCTATAGGTTTTATCATTTT
| || ||| || | |||||||||||||| || ||| |||||||||||| || |||||||||| || || ||||| || |||||| |||||||||| |||| ||||||||||||||||||||| ||||| || ||||||||||||| ||||||||| | |||||||| |||||||||||| | ||||
ctttccttttttctgatcatagaggagccgtatgaagctaaggtttcatgtacggttttggaatagcggtgggaactgtgatgttatcatcgactatgatTATCTAATAGTTCAAGTACAGTTGATATAGTTGAAGCACAGTCCAAATATGGTTTTTTTGGATGGAATCTTTGGCGTCAGCCTATAGGTTTTCTAGTTTT
upper sequence: ATCG01100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G444541_T03 (Zea mays), 3'ss of exon 1
ttagatttatttatggcccccgaggagccgtatgaggccaagacctcatgtacggttctgaaatagcggtgaaaatagtaatgttctcgccgactaggatTATCTAACAGTTTAAGTACAGTTGATATAGTTGAGGCACAATCAAAATATGGTTTTTGGGGATGGAATTTGTGGCGTCAACCTATAGGTTTTATCATTTT---------------------
|||||||||||||| || ||| |||||||||||| || |||||||||| || || ||||| || |||||| |||||||||| |||| ||||||||||||||||||||| ||||| || ||||||||||||| ||||||||| | |||||||| |||||||||||| | ||||
---------------------gaggagccgtatgaagctaaggtttcatgtacggttttggaatagcggtgggaactgtgatgttatcatcgactatgattatctaatagttcaagtacagTTGATATAGTTGAAGCACAGTCCAAATATGGTTTTTTTGGATGGAATCTTTGGCGTCAGCCTATAGGTTTTCTAGTTTTTCTAATTTCTTCTTTGGCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgtacggttctgaaatagcggtgaaaatagtaatgttctcgccgactaggatTATCTAACAGTTTAAGTACAGTTGATATAGTTGAGGCACAATCAAAATATGGTTTTTGGGGATGGAATTTGTGGCGTCAACCTATAGGTTTTATCATTTT
ttctcgcc CT-rich tract
aaaatagtaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagatttatttatggcccccgaggagccgtatgaggccaagacctcatgtacggttctgaaatagcggtgaaaatagtaatgttctcgccgactaggatTATCTAACAGTTTAAGTACAGTTGATATAGTTGAGGCACAATCAAAATATGGTTTTTGGGGATGGAATTTGTGGCGTCAACCTATAGGTTTTATCATTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - cccccga
- - - - - - - - - - - - - - - - - - - caagacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaata