Sequence
atgc intronic sequence ATGC exonic sequence...gttaattgctgattgttggattacttaacctcagttatgcaaatgtagtgtacatcatatcaatattttgagctatatatgcattttacctgtattatagGACTACGACCCATATGAGGAAAATCCTGGCACTGCTCCTTTTAGCGAACCTGAGGCTCAGATCATGCGAGAGCTATCCAAGTCATTTAAACCACATATGT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g02710.4 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g02710.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G006069_T01 (Zea mays), 3'ss of exon 6
------gttaattgctgattgttggattacttaacctcagttatgcaaatgtagtgtacatcatatcaatattttgagctatatatgcattttacctgtattatagGACTACGACCCATATGAGGAAAATCCTGGCACTGCTCCTTTTAGCGAACCTGAGGCTCAGATCATGCGAGAGCTATCCAAGTCATTTAAACCACATATGT
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tttgactttacatgtttcttgttgggtc---caatcgaagccactcaaatatgcatgttattagcctattgatttta--tgtgtgtggatttt-catgtattgtagGACTACGACCCATACGAGGAGAATCCTGGTATTGCTCCTTTTAGCGAACCTGAGGCCCAGATCATGAGGGAATTATCAAGGTCGTTTAAACCTCATATTT
upper sequence: LOC_Os02g02710.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0122g01410.t01 (Vitis vinifera), 3'ss of exon 6
gtta-attgctgattgttggattacttaacctcagttatgcaaatgtagtgtacatcatatca-atattttgagctatatatgcattttacctgtattatagGACTACGACCCATATGAGGAAAATCCTGGCACTGCTCCTTTTAGCGAACCTGAGGCTCAGATCATGCGAGAGCTATCCAAGTCATTTAAACCACATATGT
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gttgtattgcaaatt-cagtgttatgttgttt-ggtggtgggacttttccgttctttttcttttatcatttaatttttctatctctgattctttaattatagGATTATGATCCATATGAAGAAAATCCTGGAACTGCTCCTTTTAGTGAGCCTGAGACTCAAATAATGCGGAAACTCTCCATATCATTTGATCCACATATATMapped 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|58685947|gb|CK074634.1|CK074634EST: GGGGAAAGAAGGAAAAG GACTACGACCCATATGAGGAAAATCCTGGCACTGCTCCTTTTAGCGAACCT
genomic: GGGGAAAGAAGGAAAAGgttgttttct ... tgtattatagGACTACGACCCATATGAGGAAAATCCTGGCACTGCTCCTTTTAGCGAACCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtgtacatcatatcaatattttgagctatatatgcattttacctgtattatagGACTACGACCCATATGAGGAAAATCCTGGCACTGCTCCTTTTAGCGAACCTGAGGCTCAGATCATGCGAGAGCTATCCAAGTCATTTAAACCACATATGT
ttttacct CT-rich tract
atcatatcaatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaattgctgattgttggattacttaacctcagttatgcaaatgtagtgtacatcatatcaatattttgagctatatatgcattttacctgtattatagGACTACGACCCATATGAGGAAAATCCTGGCACTGCTCCTTTTAGCGAACCTGAGGCTCAGATCATGCGAGAGCTATCCAAGTCATTTAAACCACATATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT