Sequence
atgc intronic sequence ATGC exonic sequenceGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttcagcattaacatcctaagatgccatgtaccatgcatagcttactgacccacccgactaaaaacatagccttgctagtca...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g74520.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G044369_T01 (Zea mays), 5'ss of exon 2
GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttcagcattaaca--tcctaagatgccatgtaccatgcatagcttactgacccacc--cgactaaaaacatagccttgctagtca-
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GCTTATTTCCAAGCTGAACCCCTTTCCGGGGATGAAGCATCTCGATGTGTCTGGTGGAACAGgtaatatttatctccttccctcattgccagtagtttttttagtggcggacatttgtagtaggaaaaaaattcgtcgactgttcatgtcattgttttgact-tcag
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G065210_T03 (Zea mays), 5'ss of exon 4
GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttca--gcattaacatcctaagatgccatgtaccatgcatagctt-actgacccacccgac--taaaaacatagccttgctagtca
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GCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatctccttccctcattgctttcagatgcaccatagaaacaacaaatgcaaatttttactagtatcttaaacattattaattctaccttgat-----
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G438673_T02 (Zea mays), 5'ss of exon 3
GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttcagcattaacatcctaagatgccatgtaccatgcatagcttactgacccacccgactaaaaacatagccttgctagtca-
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GCTTATTTCCAAGCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAGgtaatatctatccccttctctcattgctttcagatgcaccatagaaataacaaataca-cttttttactagtatcataaacattattaattctatcttgat
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G22890.1 (Glycine max), 5'ss of exon 3
GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttct--taccttcagcattaacatcctaagatgccatgtaccatgcatagcttactgacccacccgactaaaaacatagccttgctagtca---
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GTTAGTTTCCAAGCTGAATCCGTTTCCTGGAATGAAGCATCTTGATGTGGCTGGTGGAACAGgtctgtttcattgtcactatgttttatactg-tgtcttctg-tgtagtagattttaga-agattgcaatgcgagttaaattgatgc--agtctggcaaaatatgt
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G03210.2 (Glycine max), 5'ss of exon 2
GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttcagcattaacatcctaagatgccatgtaccatgcatagcttactgacccacccgactaaaa---acatagccttgctagtca-----
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GTTAGTTTCGAAGCTGAATCCATTTCCTGGAATGAAGCATCTTGATGTTGCTGGTGGCACAGgt-ctgttacattttcactat--gtttta---tactgtctttctgtgtataggttttagaagattg--caatgcgagttaaattgatgcagtctggaaaaatatgtta
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv16s0039g01590.t01 (Vitis vinifera), 5'ss of exon 4
GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgt-attcttcctttcttaccttcagcat-taacatcctaagatgccatgtaccatgcatagcttac-tgacccacccgactaaaaacatagccttgctagtca
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GTTGGTCTCTAAATTGCATCCATTTCCTGGAATGAAGCATCTTGATGTGGCTGGTGGAACAGgttagcataccttgtacaattattatatgtagtctttttgcttggtgttttaggtagatagggtaaatgattgagggagctcaaca-aggatggggcaaga--Mapped 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|55408176|gb|CV720552.1|CV720552EST: GCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG GGGATGTTGCCTTCCGTGCGCTCGAGAGAATCAATAGCGTGAGCCATAGAG
genomic: GCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcc ... atgccttcagGGGATGTTGCCTTCCGTGCGCTCGAGAGAATCAATAGCGTGAGCCATAGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAGgtattcttcctttcttaccttcagcattaacatcctaagatgccatgtaccatgcatagcttactgacccacccgactaaaaacatagccttgctagtca
- - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA