Sequence
atgc intronic sequence ATGC exonic sequencegtttctcaacttcttctactccagaatttatcagcactgtaaatcacttgaatccatctgtttttctaacccatgacgtgcaatactcgactttcagCAAGTATATGCATACTTCCGAGGGAGTGGCAAAGCTGCAGAGATGAAGCGTGAAGCTACAAAATCGACCTTGATGCGTGCACTATGAAGAAATCACTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03550.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03550.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------------------------------gtttctc-aacttcttctactccagaatttatcagcactgtaa--atcacttgaatccatctgtttttctaacccatgacgtgcaatactcg-actttcagCAAGTATATGCATACTTCCGAGGGAGTGGCAAAGCTGCAGAGATGAAGCGTGAAGCTACAAAATCGACCTTGATGCGTGCA-CTATGAAGAAATCACTCTT--
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gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattc-tcaagtagtctatctgagccgttttgacatttgtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCT---ATGCGGGCAGCTTTTTAATTATCAGAAAAGA
upper sequence: AT1G03550.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------------------------------gtttctcaacttcttctactccagaatttatcagcactgtaaat-cacttgaatccatctgtttttctaacccatgacgtgcaatactcgactttcagCAAGTATATGCATACTTCCGAGGGAGTGGCAAAGCTGCAGAGATGAAGCGTGAAGCTACAAAATCGACCTTGATGCGTGCACTATGAAGAAATCACTCTT
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gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattat--tgttctgaacttg--tttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
upper sequence: AT1G03550.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gtttctcaacttcttctactccagaatttatcagcactgtaaatcacttgaatccatctgtttttctaacccatga-cgtgcaatactcgactttcagCAAGTATATGCATACTTCCGAGGGAGTGGCAAAGCTGCAGAGATGAAGCGTGAAGCTACAAAATCGACCTTGATGCGTGCACTATGAAGAAATCACTCTT
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--------------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcacttgaatccatctgtttttctaacccatgacgtgcaatactcgactttcagCAAGTATATGCATACTTCCGAGGGAGTGGCAAAGCTGCAGAGATGAAGCGTGAAGCTACAAAATCGACCTTGATGCGTGCACTATGAAGAAATCACTCTT
ttctaac putative branch site (score: 1)
ctttc putative PPT
tttttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttctcaacttcttctactccagaatttatcagcactgtaaatcacttgaatccatctgtttttctaacccatgacgtgcaatactcgactttcagCAAGTATATGCATACTTCCGAGGGAGTGGCAAAGCTGCAGAGATGAAGCGTGAAGCTACAAAATCGACCTTGATGCGTGCACTATGAAGAAATCACTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA