Sequence
atgc intronic sequence ATGC exonic sequence...ccctagtattttctacataaattagtgatgaatactcatattacttttccatgttcttattctatatatcactactaataaaatatcctaacttccgcagCTGCATTTGGAGGCGTCCTTCATGTTGTTTCCACTGCTCTTCTTGGGATAACTGCTGTTACTATGGCAAATACTATAGCAGGCGAGGAAACAGTGCATAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17020.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G078895_T02 (Zea mays), 3'ss of exon 1
ccctagtattttctacataaattagtgatgaatactcatattacttttccatgttcttat-tctatat-atcactactaataaaatatc-ctaacttccgcagCTGCATTTGGAGGCGTCCTTCATGTTGTTTCCACTGCTCTTCTTGGGATAACTGCTGTTACTATGGCAAATACTATAGCAGGCGAGGAAACAGTGCATAA
| || | | | | | | | | | | | | ||| ||| ||| | ||||||| || |||| | |||| || |||||||| ||||||||||||||||| || |||||||||||||| || |||||||||||||||||||| ||||||||||||||||||||||| ||||| ||||||||||||||
--caagaacctgcaatttca-tattttccaattttttaaattttcaaatgatgcccttctctctatatgattgttactgagaaaagattactaacttctgcagCTGCATTTGGAGGTGTTCTTCATGTTGTTTCTACGGCTCTTCTTGGGATAACTGCAGTTACTATGGCAAATACTATAGCTGGCGAAGAAACAGTGCATAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86822669|gb|CI251769.1|CI251769EST: GTGGCCGCTCTCCCGCACCCTCCTCGTCA CTGCATTTGGAGGCGTCCTTCATGTTGTTTCCACTGCTCTTCTTGGGATAA
genomic: GTGGCCGCTCTCCCGCACCCTCCTCGTCAgtcagtatcc ... acttccgcagCTGCATTTGGAGGCGTCCTTCATGTTGTTTCCACTGCTCTTCTTGGGATAA
EST:
gi|33819859|gb|CF335746.1|CF335746EST: CATCGTCGCCCGCGCCCAGCGGTGGCCGCTCTCCCGCACCCTCCTCGTCA CTGCATTTGGAGGCGTCCTTCATGTTGTTTCCACTGCTTTTCTTGGGATAA
genomic: CATCGTCGCCCGCGCCCAGCGGTGGCCGCTCTCCCGCACCCTCCTCGTCAgtcagtatcc ... acttccgcagCTGCATTTGGAGGCGTCCTTCATGTTGTTTCCACTGCTCTTCTTGGGATAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccatgttcttattctatatatcactactaataaaatatcctaacttccgcagCTGCATTTGGAGGCGTCCTTCATGTTGTTTCCACTGCTCTTCTTGGGATAACTGCTGTTACTATGGCAAATACTATAGCAGGCGAGGAAACAGTGCATAA
tcctaac putative branch site (score: 1)
cttccgc CT-rich tract
ttattctatatatcac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccctagtattttctacataaattagtgatgaatactcatattacttttccatgttcttattctatatatcactactaataaaatatcctaacttccgcagCTGCATTTGGAGGCGTCCTTCATGTTGTTTCCACTGCTCTTCTTGGGATAACTGCTGTTACTATGGCAAATACTATAGCAGGCGAGGAAACAGTGCATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - acataaa
- - - - - - - - - - - - -tgatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa