Sequence
atgc intronic sequence ATGC exonic sequence...tcttcatgaaagcatcttgttatacagaggctcattcatggattttgtatagaattgctaaattggtagttcttttgtccatacctgtgatctcatgcagGATTGGCAGCCTGCCTATTTTGGAATATCATAGCAACCACAACCGCATGGGTAAAAGGGGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g42330.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 5
tcttcatgaaagcatcttgttatacagaggctcattcatggattttgtatagaattgctaa-----attggtagttcttttgtcc-atacctgtgatctcatgcagGATTGGCAGCCTGCCTATTTTGGAATATCATAGCAACCACAACCGCATGGGTAAAAGGGGAAG
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--tagactgatgcatttcac-ataaaaaaattc--tgatagatagtgtctagtgcttccatttggcatctgtggttttcttacccgatgcttgtt-cctcatgaagGATTGATAGCGTGCCTCTTTTGGAATATCATAGCAACTACAACAGCATGGATTAAAGGGGAAG
upper sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 5
tcttcatgaaagcatcttgttatacagaggctcattcatggattttgtatagaattgctaaattggtagttcttttgtcc-atacctgtgatc-tcatgcagGATTGGCAGCCTGCCTATTTTGGAATATCATAGCAACCACAACCGCATGGGTAAAAGGGGAAG
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-tcacagaaaatagttctgatagatagtgtctagtacattgaattggcatagcatttctcaaccga-ggttctcttacccgatgcttgttccccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtatagaattgctaaattggtagttcttttgtccatacctgtgatctcatgcagGATTGGCAGCCTGCCTATTTTGGAATATCATAGCAACCACAACCGCATGGGTAAAAGGGGAAG
tgctaaa putative branch site (score: 2)
taaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttcatgaaagcatcttgttatacagaggctcattcatggattttgtatagaattgctaaattggtagttcttttgtccatacctgtgatctcatgcagGATTGGCAGCCTGCCTATTTTGGAATATCATAGCAACCACAACCGCATGGGTAAAAGGGGAAG
-cttcatg
- - - - - - - - - - - - - - - - -attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgtga