Sequence
atgc intronic sequence ATGC exonic sequence...ctactaacatctattgtttttcatttgtggaactgctttcacatttctctatttgattgtatagagtatactcacatgttaacggtgtctttgttaacagTTTCACCAGGTACAGAAGGCACTGATTCTGGCTTGGCATCAGTTCTAAATTCACTGGAGTTCTGCCTAAAACCTTGTGGTTCTGAAGCTAGTATACTAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g21780.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G116196_T01 (Zea mays), 3'ss of exon 7
--ctactaacatctattgtttttcatttgtggaactgctttcacatttctctatttgattgtatagagtatactcacatgttaacggtgtctttgttaacagTTTCACCAGGTACAGAAGGCACTGATTCTGGCTTGGCATCAGTTCTAAATTCACTGGAGTTCTGCCTAAAACCTTGTGGTTCTGAAGCTAGTATACTAGA
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cagcagtacagcacatgttacttgatttgtc-aactgttttggcatcctccttcctgaat-tgtcgtgtatactcacatgtttctcatatcctgattaatagTTTCACCAGGTACAGAAGGCACAGATTCTGGCTTGGCTTCAGTATTAAATTCACTGGAGTTCTGCCTAAAACCATGTGGGTCTGAAGCTAGCATATTAGA
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G055917_T01 (Zea mays), 3'ss of exon 7
ctactaacatctattgtttttcatttgtggaactgctttcacatttctctatttgattgtatagagtatactcacatgttaacggtgtctttgttaacagTTTCACCAGGTACAGAAGGCACTGATTCTGGCTTGGCATCAGTTCTAAATTCACTGGAGTTCTGCCTAAAACCTTGTGGTTCTGAAGCTAGTATACTAGA---------
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------acagacgtcattt--gatttatc-atctgttttggcatgtctcttcctgaatcgcaataatatactcacatatttctcatatccttattaatagtttcaccagGTACAGAAGGCACAGATTTTGGCTTGGCTTCAGTATTAAATTCACTGGAGTTCTGTCTAAAGCCTTGTGGGTCTGAAGCTAGCATATTAGAGGATTTATC
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G055917_T02 (Zea mays), 3'ss of exon 7
ctactaacatctattgtttttcatttgtggaactgctttcacatttctctatttgattgtatagagtatactcacatgttaacggtgtctttgttaacagTTTCACCAGGTACAGAAGGCACTGATTCTGGCTTGGCATCAGTTCTAAATTCACTGGAGTTCTGCCTAAAACCTTGTGGTTCTGAAGCTAGTATACTAGA
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cttcttacaacagacgtcatttgatttatcatctgttttggcatgtctcttcctgaatcgcaataatatactcacatatttctcatatccttattaatagTTTCACCAGGTACAGAAGGCACAGATTTTGGCTTGGCTTCAGTATTAAATTCACTGGAGTTCTGTCTAAAGCCTTGTGGGTCTGAAGCTAGCATATTAGAMapped 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|88340089|gb|CI650536.1|CI650536EST: GTGCCATCCATATGCCGCATCTCTACTGCTCTTCAGTACAATTCT-G--- TTTCACCAGGTACAGAAGGCACTGATTCTGGCTTGGCATCAGTTCTAAATT
genomic: GTGCCATCCATATGCCGCATCTCTACTGCTCTTCAGTACAATTCTGGCAAgttcactgct ... ttgttaacagTTTCACCAGGTACAGAAGGCACTGATTCTGGCTTGGCATCAGTTCTAAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctatttgattgtatagagtatactcacatgttaacggtgtctttgttaacagTTTCACCAGGTACAGAAGGCACTGATTCTGGCTTGGCATCAGTTCTAAATTCACTGGAGTTCTGCCTAAAACCTTGTGGTTCTGAAGCTAGTATACTAGA
tctttgtt CT-rich tract
atttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctactaacatctattgtttttcatttgtggaactgctttcacatttctctatttgattgtatagagtatactcacatgttaacggtgtctttgttaacagTTTCACCAGGTACAGAAGGCACTGATTCTGGCTTGGCATCAGTTCTAAATTCACTGGAGTTCTGCCTAAAACCTTGTGGTTCTGAAGCTAGTATACTAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC