Sequence
atgc intronic sequence ATGC exonic sequence...gtcaacatcttcagaaactaggacatttgtttgtgagaatgatgatatatcacttccatctttttatgcttttctaagttggttttcgtatgtgttgtagTGGTTTGCTGTAACACGAAGGCATGCTTTACTGATTTTAGCAGACCACCTTTACTACAATAAGTTCGAGCTGTATTGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g07880.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------gtcaacatcttcagaaactaggacatttgtttgtgagaatgatgatatatcacttccatctttttatgcttttctaagttggtt-ttcgtatgtgttgtagTGGTTTGCTGTAACACGAAGGCATGCTTTACTGATTTTAGCAGACCACCTTTACTACAATAAGTTCGAGCTGTATTGCAAG
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gtacatgtttaatagaatattagaatgattggtgcttcaaaatattcatcattctgttgttttataatcgctgtctt--ataatcaggacatg-gcagttcatattgatgcgcgatca----cattttttcatgcttttgttgaatatttatttgtgcttgctgcagTGGTTTGCTATAACACGAAGGCATGCTTTATTGATTCTGGCAGACAACCTTTACTACAATAAGTTCAAGCTGTACTGCAAG
upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------gtcaacatcttcagaaactaggacatttgtttgtgagaatgatgatatatcacttccatctttttatgctttt-ctaagttggttttcgtatgtgttgtagTGGTTTGCTGTAACACGAAGGCATGCTTTACTGATTTTAGCAGACCACCTTTACTACAATAAGTTCGAGCTGTATTGCAAG
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gtatatgtttgctatactatctgtatttaatagaatgattgatgcttcaaattagatatctgtatgtattcataattctgcccgtcgtataatcaggaca--tggcagttcgtattgatgtgtgtcacat---ttttttcatgattttgctgaatatttttttgtgcttgctgtagTGGTTTGCTATAACACGAAGGCATGCTTTATTGATTCTGGCTGACAACCTTTACTACAATAAGTTCAAGCTGTACTGCAAGMapped 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|29662011|gb|CB658286.1|CB658286EST: AGGAAGGGTGCCCAG TGGTTTGCTGTAACACGAAGGCATGCTTTACTGATTTTAGCAGACCACCTT
genomic: AGGAAGGGTGCCCAGgttcatattt ... tgtgttgtagTGGTTTGCTGTAACACGAAGGCATGCTTTACTGATTTTAGCAGACCACCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatcacttccatctttttatgcttttctaagttggttttcgtatgtgttgtagTGGTTTGCTGTAACACGAAGGCATGCTTTACTGATTTTAGCAGACCACCTTTACTACAATAAGTTCGAGCTGTATTGCAAG
atctttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaacatcttcagaaactaggacatttgtttgtgagaatgatgatatatcacttccatctttttatgcttttctaagttggttttcgtatgtgttgtagTGGTTTGCTGTAACACGAAGGCATGCTTTACTGATTTTAGCAGACCACCTTTACTACAATAAGTTCGAGCTGTATTGCAAG
- - -catcttc
- - - - - - -gaaacta
- - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - atgatga