Sequence
atgc intronic sequence ATGC exonic sequence...tagattagataagcatttttttttaaaaaaaattagccctttttcttcagtttgtgctcttttggatgctttgtatggtttcatcatttattttctgcagGCATATATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGATAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g59350.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G125243_T01 (Zea mays), 3'ss of exon 6
-tagattagataagcatttttttttaaaaaaaattagccctttttcttcagtttgtgctcttttggatgctttgtatggtttcatcatttattttctgcagGCATATATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGATAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG
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taaggctatggtattactttcccccctttacatctatttatcttttgttgcatcattttggtagaattaatttgcacc-cttcaccttatgttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G125243_T02 (Zea mays), 3'ss of exon 8
--------------------tagattagataagcattttt-----ttttaaaaaaaattagccctttttcttcagtttgtgctcttttggatgctttgtatgg--------------tttcatcatttattttctgcagGCATATATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGATAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG
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gtgccagcagctgtagaatgtagatcacattagcatttttaaggctatggtattactttcccccctttacatctatttatcttttgttgcatcattttggtagaattaatttgcacccttcaccttatgttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G019907_T01 (Zea mays), 3'ss of exon 2
tagattagataagcatttttttttaaaaaaaattagccctttttcttcagtttgtgctcttttggatgctttgtatggt----ttcatcatttattttctg-cagGCATATATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGATAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG
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----tttggctatgatactattacccccacccccatctacttctcttttgtt-gcatcatttggtagaattaattttgcacccttcaccttatgttttctttcagGCATACATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGTTAGAGCAAGAGCTTCACCAGACTCGTCAACAG
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ22847 (Selaginella moellendorffii), 3'ss of exon 1
tagattagataagcatttttttttaaaaaaaattagccctttttcttcagtttgtgctcttttggatgctttgtatggtttcatcatttattttctgcagGCATATATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGATAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG
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-------------------------------------gtataattcccatcttcttttctttgaagaacatattactaagtagaaacttat---aaacagGCATACGTTCAGCAGCTTGAATCGAGCCGGATGAAACTAAACCAGCTCGAGCAAGAGCTTCAGCGCGCTCGTCAACAGMapped 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|33793551|gb|CF322658.1|CF322658EST: GCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAG GCATATATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGATAGAG
genomic: GCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAGgtgtgtttgt ... ttttctgcagGCATATATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGATAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagtttgtgctcttttggatgctttgtatggtttcatcatttattttctgcagGCATATATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGATAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG
tttattttct CT-rich tract
tttcatcatttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagattagataagcatttttttttaaaaaaaattagccctttttcttcagtttgtgctcttttggatgctttgtatggtttcatcatttattttctgcagGCATATATCCAAAACCTTGAGAGTAGCAGATTGAAACTTACTCAGATAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT