Sequence
atgc intronic sequence ATGC exonic sequence...attatcttactaatttgtcacatacctattgggtacatacatagattcagagttctctgaaactgctaacattatgtctgaactcaaattgcaatttcagTTCTACTGCTGGGCACAAGAGTGGCAGCATCAGCCGCAGCGATCTCCCCTGCATCGGAGAAGAAAGCCTGGCTGATCCTGGCCTGGGTGAGCACGGTGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g31040.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G347174_T02 (Zea mays), 3'ss of exon 3
attatcttactaatttgtcacatacctattgg-gtacatacatagattcagagttctctgaaactgctaacattatgtctgaactcaaattgcaatttcagTTCTACTGCTGGGCACAAGAGTGGCAGCATCAGCCGCAGCGATCTCCCCTGCATCGGAGAAGAAAGCCTGGCTGATCCTGGCCTGGGTGAGCACGGTGGC
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---------------------------gttggtatatatatattcagtctgaacattc-gaaacatctgacaa-agatctgagacttcgtttccgatccagTCCTCCTGCTGGGCTCCAGAGTGGCAGCGTCAGCGGCTGCCATCTCCCCGGAGTCGCAGAAGAAAGCCTGGCTCATACTAGCGTGGGTCAGCACGGTGTC
upper sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G060742_T02 (Zea mays), 3'ss of exon 3
--attat-cttactaatttgtcacatacctattgggtacatacatagattcagagttctctgaaactgctaacattatgtctgaactcaaattgcaa------tttcagTTCTACTGCTGGGCACAAGAGTGGCAGCATCAGCCGCAGCGATCTCCCCTGCATCGGAGAAGAAAGCCTGGCTGATCCTGGCCTGGGTGAGCACGGTGGC
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gtacgatacgtactg-ctcatggcgtacacgttgcttaccttctttaatctgttctcaaatgtgactgctgaatgtatgtacgtatatatatttgaaacttcctttcagTTCTTCTGCTGGGCACAAGGGTGGCAGCGTCAGCAGGCACAATCTCCCCAGAGTCAGAGAAGAAAGCCTGGCTCATACTAGCATGGGTGAGCACGGTGGC
upper sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ26576 (Selaginella moellendorffii), 3'ss of exon 3
attatcttactaatttgtcacatacctattgggtacatacatagattcagagttctctgaaactgctaacattatgtctgaactcaaattgcaatttcagTTCTACTGCTGGGCACAAGAGTGGCAGCATCAGCCGCAGCGATCTCCCCTGCATCGGAGAAGAAAGCCTGGCTGATCCTGGCCTGGGTGAGCACGGTGGC
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--------------------------------gtaagtttggaaggacgagagtattcttctttgct--catgatctcttctttctggttttcattctagTTCTTCTCTTGGGTGCTCGAGTAGCAGCCTCGGCCGCCGCAACCGAGGGAGCGAGCGTGAAGAAAGCGTGGCTGATCCTCGCCTGGGTGAGCACCGTGGC
upper sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ14830 (Selaginella moellendorffii), 3'ss of exon 3
attatcttactaatttgtcacatacctattgggtacatacatagattcagagttctctgaaactgctaacattatgtctgaactcaaattgcaatttcagTTCTACTGCTGGGCACAAGAGTGGCAGCATCAGCCGCAGCGATCTCCCCTGCATCGGAGAAGAAAGCCTGGCTGATCCTGGCCTGGGTGAGCACGGTGGC
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----------------------------------gtaagtttggaaggagagcattcttct-ttgct--catgatctcttctttttggatttcattctagTTCTTCTCTTGGGTGCTCGAGTAGCAGCCTCGGCCGCCGCAACCGAGGGAGCGAGCGTGAAGAAAGCGTGGCTGATCCTCGCCTGGGTGAGCACCGTGGCMapped 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|33680059|gb|CF308298.1|CF308298EST: CGCGATCGTCATCCTTGTTCTGTCAAATTTGGCATCAAATGTTCCAACAG TTCTACTGCTGGGCACAAGAGTGGCAGCATCAGCCGCAGCGATCTCCCCTG
genomic: CGCGATCGTCATCCTTGTTCTGTCAAATGTGGCATCAAATGTTCCAACAGgtaaagaaaa ... gcaatttcagTTCTACTGCTGGGCACAAGAGTGGCAGCATCAGCCGCAGCGATCTCCCCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagagttctctgaaactgctaacattatgtctgaactcaaattgcaatttcagTTCTACTGCTGGGCACAAGAGTGGCAGCATCAGCCGCAGCGATCTCCCCTGCATCGGAGAAGAAAGCCTGGCTGATCCTGGCCTGGGTGAGCACGGTGGC
tgctaac putative branch site (score: 1)
taacattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attatcttactaatttgtcacatacctattgggtacatacatagattcagagttctctgaaactgctaacattatgtctgaactcaaattgcaatttcagTTCTACTGCTGGGCACAAGAGTGGCAGCATCAGCCGCAGCGATCTCCCCTGCATCGGAGAAGAAAGCCTGGCTGATCCTGGCCTGGGTGAGCACGGTGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT