Sequence
atgc intronic sequence ATGC exonic sequenceCGGCGGCGGGATGTACGTGCCGCAGCCATCTCGCTCCGATGCGGCCGGCCGCGACGCCGGCGACCAGCCTAGGGTTTACCAGGTTTGGCGGGGAAGCAACgtaagcactctctctctctctctctctctccctctctctctcgcctttgccgcagggtgaagctggagctggatctgtacttagcggcgcactatgcgca...
Basic information
species | Oryza sativa |
transcript | LOC_Os08g42370.3 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G068657_T02 (Zea mays), 5'ss of exon 1
CGGCGGCGGGATGTACGTGCCGCAGCCATCT-CGCTCCGATGCGGCCGGCCG-CGACGCCGGCGACCAGCCTAGGGTTTACCAGGTTTGGCGGGGAAGCAACgtaagcactctctctctctctctctctctccctctctctctcgcctttgccgcagggtgaagctggagctggatctgtacttagcggcgcactatgcgca----
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--GCCACCTGCCCCCTGCGCCGTCGGGATGTACGTGCCGCCGCCGCCCACCGGCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatctctacctgccaccctccttttctctccccatc----tggccgcagtggtccgtgcgacgttgatgggattgtaactgctgatttcgccccgtac
upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 1
------------CGGCGGCGGGATGTACGTGCCGCAGCCATCTCGCTCCGATGCGGCCGGCCGCGACGCCGGCGACCAGCCTAGGGTTTACCAGGTTTGGCGGGGAAGCAACgtaagcactctctctctctctctctctctccctctctctctcgcctttg--ccgcagggtgaagctggagctggatctgtacttagcggcgcactatgcgca-
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CCCCCTCCCCTGCGCCGTCGGGATGTACATGCCGCCGCCGCCGCCCACCG------------GCGGCGCCGGCGAGCAGCCTAGGCTTTACCAGGTCTGGCGGGGAAGCAACgtaagaaatttctacctgccacccgctcttcctctccccatatgcagtgatccgtgagatgttgatggaagtgta---ataatcgattttgctcagtacctgtMapped 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|29656638|gb|CB652913.1|CB652913EST: GCCACGCCGGCGACCAGCCTAGGGTTTACCAGGTTTGGCGGGGAAGCAAC TGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCG
genomic: GCGACGCCGGCGACCAGCCTAGGGTTTACCAGGTTTGGCGGGGAAGCAACgtaagcactc ... gttgcaccagTGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGGCGGCGGGATGTACGTGCCGCAGCCATCTCGCTCCGATGCGGCCGGCCGCGACGCCGGCGACCAGCCTAGGGTTTACCAGGTTTGGCGGGGAAGCAACgtaagcactctctctctctctctctctctccctctctctctcgcctttgccgcagggtgaagctggagctggatctgtacttagcggcgcactatgcgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA