Sequence
atgc intronic sequence ATGC exonic sequenceATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCAgtaagtgatactttatcaaatcacaacaccctaataaagttactactgaaaaaaagtttcatgtatacatgaagtttttctaaacggttttcttgaatga...
Basic information
species | Oryza sativa |
transcript | LOC_Os05g50170.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G406177_T01 (Zea mays), 5'ss of exon 5
ATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCAgtaagtgatactttatcaaatcacaacaccc--taataa----agttactactgaaaaaaagtttcatgtatacatgaagtttttctaaacggttttcttgaatga-------------------
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ATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGCGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAATAAgtaagtgatactttgacatttgtttgcaagtagtagtacttacagttgttctttgagcatctctactttagatcctgtattttaattgttaacttttaataaatgaatttatgatgaatctgtag
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G325504_T01 (Zea mays), 5'ss of exon 2
ATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCAgtaagtgatactttatcaaatcacaacaccc--taataa----agttactactgaaaaaaagtttcatgtatacatgaagtttttctaaacggttttcttgaatga-------------------
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ATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGCGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAATAAgtaagtgatactttgacatttgtttgcaagtagtagtacttacagttgttctttgagcatctctactttagatcctgtattttgattgttaatttttaataaatgaatttatgatgaatctgtag
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G437845_T01 (Zea mays), 5'ss of exon 6
ATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCAgtaagtgatactttatcaaatcacaacaccc--taataa----agttactactgaaaaaaagtttcatgtatacatgaagtttttctaaacggttttcttgaatga-------------------
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ATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGTGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAATAAgtaagtgatactttgacatttgtttgcaagtagtagtacttatagttgttcgttgagcatctctactttagatcctgtattttgattgttaacttttaataaatgaatttatgatgaatctgtag
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G427351_T01 (Zea mays), 5'ss of exon 7
ATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCAgtaagtgatactttatca---aatcacaac--accctaataaagttactactgaaaaaaagtttcatgtatacatgaagtttttctaaacggttttct-tgaatga-------------------
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ATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGCGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAATAAgtaagtgatactttgacatttgtttgcaagtagtagtacttacggttgttctttgagcatctctactttagatcctatattttgattgttaacttttaataaatgaatttatgatgaatctgtag
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G854930_T01 (Zea mays), 5'ss of exon 8
ATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCAgtaagtgatactttatcaaatcacaacaccc--taataa----agttactactgaaaaaaagtttcatgtatacatgaagtttttctaaacggttttcttgaatga-------------------
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ATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGCGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAATAAgtaagtgatactttgacatttgtttgcaagtagtagtacttacagttgttctttgagcatctctactttagatcttgtattttgattgttaacttttaataaatgaatttatgatgaatccgtagMapped 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|66926863|gb|CX113711.1|CX113711EST: ATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCA GATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCT
genomic: ATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCAgtaagtgata ... aatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCAgtaagtgatactttatcaaatcacaacaccctaataaagttactactgaaaaaaagtttcatgtatacatgaagtttttctaaacggttttcttgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa