Sequence
atgc intronic sequence ATGC exonic sequence...attgttccctttttttgccggcaccagttgtgctagtttgaattagggtacccttcttcagagttaacacatctaccccttttcctgccattgttaaaagCATAAAAATGAGGTGGTGAATGAGGAACTTTGGAATGAAGCACGAACATATGGAGACATCCAATTGATGCCCTTTGTTGATTATTATAGCCTGATTCTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g12390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G164072_T01 (Zea mays), 3'ss of exon 3
-------attgttccctttttttgccggcaccagttgtgctagtttgaattagggtacccttcttcagagttaacacatctaccccttttcctgccattgttaaaagCATAAAAATGAGGTGGTGAATGAGGAACTTTGGAATGAAGCACGAACATATGGAGACATCCAATTGATGCCCTTTGTTGATTATTATAGCCTGATTCTAT
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ctccaagaaagttggaatgatttataatctggaacagagggagtatatgtta---tacttttctacc--ctttactcatctggcccta--ccttccattgttaaaagCACAAAAACGAGGTGGTCAATGAGGAACTCTGGAATGAAGCACGAACATATGGAGACATCCAGTTGATGCCATTTGTGGATTACTATAGCCTGATTCTTT
upper sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G042607_T01 (Zea mays), 3'ss of exon 3
----attgttccctttttt-tgccggcaccagttgtgctagtttgaattagggtacccttcttcagagttaacacatctaccccttttcctgccattgttaaaagCATAAAAATGAGGTGGTGAATGAGGAACTTTGGAATGAAGCACGAACATATGGAGACATCCAATTGATGCCCTTTGTTGATTATTATAGCCTGATTCTAT
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agtcacttttctatatgttatacttctgcc--ctttactagattgaattag---atctcaatttagagtcaatactcaactgaccctactttgcattgttaaaagCACAAAAATGAGTTGGTCAATGAGGAACTCTGGAATGAAGCACGAACATATGGAGACATCCAGTTGATGCCATTTGTGGATTACTATAGCCTGATTCTTT
upper sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0108g00890.t01 (Vitis vinifera), 3'ss of exon 3
attgttccctttttttgccggcaccagttgtgctagtttgaattagggtacccttcttcag-agttaacacatctaccccttttcctgccattgttaaaagCATAAAAATGAGGTGGTGAATGAGGAACTTTGGAATGAAGCACGAACATATGGAGACATCCAATTGATGCCCTTTGTTGATTATTATAGCCTGATTCTAT
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agctactgtaaatcatacagaagtttttgctacctttttgtctcaggtttctcctgaatattagttgaaacatttgtctgaaatttgcactttgctgca-gCATAAAAATCAGATGGTGAATGAGGAACTCTGGAAGGAGGTGCAGACATATGGAGACATTCAGCTGATGCCTTTTGTTGACTATTACAGTCTTATAACCT
upper sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0026g02530.t01 (Vitis vinifera), 3'ss of exon 3
attgttccctttttttgccggcaccagttgtgctagtttgaattagggtacccttcttcagagttaaca--catctaccccttttcctgccattgttaaaagCATAAAAATGAGGTGGTGAATGAGGAACTTTGGAATGAAGCACGAACATATGGAGACATCCAATTGATGCCCTTTGTTGATTATTATAGCCTGATTCTAT
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gttgaagcctgtttttgatttatttatttct--ttgtgtgagtctgtagcctattttgagttatttattttcaatgaactaaaactttgacatgtattgcagCATAAAAATAAAATGGTGAATGAGGAACTCTGGAATGAGGCACGGACATATGGAGATACACAGTTAATGCCTTTTGTTGACTACTATAGCATCATCACTTMapped 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|27577040|gb|CA999734.1|CA999734EST: ATGATGCTGTCCGCTCAGGAAAGGCTGCAGTTCGATTCTTTGTTGGCCTG CATAAAAATGAGGTGGTGAATGAGGAACTTTGGAATGAAGCACGAACATAT
genomic: ATGATGCTGTCCGCTCAGGAAAGGCTGCAGTTCGATTCTTTGTTGGCCTGgtaagcatga ... ttgttaaaagCATAAAAATGAGGTGGTGAATGAGGAACTTTGGAATGAAGCACGAACATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggtacccttcttcagagttaacacatctaccccttttcctgccattgttaaaagCATAAAAATGAGGTGGTGAATGAGGAACTTTGGAATGAAGCACGAACATATGGAGACATCCAATTGATGCCCTTTGTTGATTATTATAGCCTGATTCTAT
agttaac putative branch site (score: 3)
tctaccccttttcctg putative PPT
attgttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgttccctttttttgccggcaccagttgtgctagtttgaattagggtacccttcttcagagttaacacatctaccccttttcctgccattgttaaaagCATAAAAATGAGGTGGTGAATGAGGAACTTTGGAATGAAGCACGAACATATGGAGACATCCAATTGATGCCCTTTGTTGATTATTATAGCCTGATTCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA