Sequence
atgc intronic sequence ATGC exonic sequenceGCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAGATTATTGGTCTTTTTGGAGTTTTTGATGgtatgtatgaatttgtcacattcgtgcataatctctacccattgataattctttatcattttagaaaggaacatttctaagattacactcttccaagttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g56450.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g56450.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G056572_T02 (Zea mays), 5'ss of exon 2
GCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAGATTATTGGTCTTTTTGGAGTTTTTGATGgtatgtatgaatttgtcacattcgtgcataatctctacccattgataattctttatcattttagaaaggaacatttctaagattacactcttccaagttt----------
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GCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAGTTGGTCTTTTTGGAGTTTTTGATGgt----acggatttctcttaagccagcatgatttagttatataatttgagcgcaactttcatctgtagccagttctttctgatcccatggcctatggtttgtttgtgtag
upper sequence: LOC_Os04g56450.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA04G06250.1 (Glycine max), 5'ss of exon 3
GCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAGATTATTGGTCTTTTTGGAGTTTTTGATGgtatgtatgaattt----gtcacattcgtgcataatctctaccc--attgataattctttatcattttagaaaggaacatttctaagattacactcttccaagttt
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GCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGAAGGTGAAATTGTTGGCCTTTTCGGAGTTTTTGATGgtatgtttataccttcctgtcttcttcatctccaggttgtacactgattggaaaacatgccaaaatattgcacgtagaactcatgctatgttactcctgt------
upper sequence: LOC_Os04g56450.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA14G12220.1 (Glycine max), 5'ss of exon 2
GCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAGATTATTGGTCTTTTTGGAGTTTTTGATGgtatgtatgaatttgtcacattcgtgcataatctc-tacccattgataattctttatcattttagaaaggaacatttctaagattacactcttcca--agttt--
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GCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAAATTGTTGGCCTTTTTGGAGTTTTTGATGgtatatttacataattctctcatctccatgtccttgtatccat-----gctacttatgttaagaaaagatgctaagatgatgattgtagttgtacattaattgat
upper sequence: LOC_Os04g56450.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 3
GCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAGATTATTGGTCTTTTTGGAGTTTTTGATGgtatgtatgaatttgtcacattcgtgcataatctc-tacccat--tgataattctttatcattttagaaagg-aacatttctaagattacactcttccaagttt
|| ||||||||||| || || |||| |||||||| ||||| ||||||| |||||| ||||||||| | ||| |||| ||||||||||||||||||||||| | | || || | | ||| || || |||| | | | | | | ||| | || || |||| | | |
GCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAAATTGTTGGCCTTTTTGGAGTTTTTGATGgtatatgtacataattctctcgtctccatgtccttgtatccatgctacttacgttaagaaaagatgctaagatgatggttgtagttgtacattaattgga----
upper sequence: LOC_Os04g56450.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 5'ss of exon 3
GCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAGATTATTGGTCTTTTTGGAGTTTTTGATGgtatgtatgaatttgtcacattcgtgcataatctctacccattgataattctttatcattttagaaaggaacatttctaagattacactcttccaagttt-----
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GCTAGTTCTCCCGGGAAAAGGTCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGAAGGAGAGATAGTTGGCCTTTTTGGAGTCTTTGATGgtac-tctttctttctctttctc-tctcttctacccatcccccaacaacactcaagcat---aggtaggtagattctgcatgcagtctttggtgtagcttgtatcMapped 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|701023|gb|D47314.1|D47314EST: AATTGACTCTGTTGATGGGCAGATTATTGGTCTTTTTGGAGTTTTTGATG GTCATGGTGGTGCTAAAGTAGCTGAGTATGTTAAACAGAATCTCTTCAGTC
genomic: AATTGACTCTGTTGATGGGCAGATTATTGGTCTTTTTGGAGTTTTTGATGgtatgtatga ... cattttatagGTCATGGTGGTGCTAAAGTAGCTGAGTATGTTAAACAGAATCTCTTCAGTC
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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAGATTATTGGTCTTTTTGGAGTTTTTGATGgtatgtatgaatttgtcacattcgtgcataatctctacccattgataattctttatcattttagaaaggaacatttctaagattacactcttccaagttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctaccc