Sequence
atgc intronic sequence ATGC exonic sequenceTCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttgagtagagtgctctaagactgttatacaactattatctttttcctgatatgccacctgttatgttgtcattattatttatactcatgcaaaa...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g53900.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AC203173.3_FGT004 (Zea mays), 5'ss of exon 1
TCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttgagtagagtgctctaagac-tgttatacaactattatctttttcctgatatgccacctgttatgttgtcattattatttatactcatgcaaaa
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---------ATGGTGAAGTTCACGGCTGAAGAGCTCCGTGCCATCATGGACAAAAAGAACAACATTCGTAATATGTCTGTTATTGCTCATGTGGACCATGgtatgttcaaa-acactactttgttagatgttatatagtccttaatatttttgagcctctttgtttttaaaatttatttcgttttcaatgtttaagagcta
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G113250_T01 (Zea mays), 5'ss of exon 2
TCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttgagtagagtgctctaagactgttatacaactattatctttttcctgatatgccacctgttatgttgtcatt-attatttatactcatgcaaaa---
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GGAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGTGCCATCATGGACAAAAAGAACAACATTCGTAACATGTCTGTTATTGCTCATGTGGACCATGgtaggttc-agaacactgccc-aagacattttgatgtcaattgttctgtttc-aatatttaagct-ttgtactgttcttgattgccgatgcttctattcatgct
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G095851_T01 (Zea mays), 5'ss of exon 2
TCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgttt-gagtagagtgctctaagactgttatacaactattatctttttcctgatatgccacctgttatgttgtcattattatttatactcatgcaaaa-
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GAAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGCGCTATCATGGACAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcagaacactgctctgtagcatatatatacatgcattg-cttaacgttttcaagcctttttatgtgtagacttaatttgctccaat-atttgagct
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S431_6V6.1 (Physcomitrella patens), 5'ss of exon 2
TCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttgagtagagtgctctaagactgttatacaactattatctttttcctgatatgccacctgttatgttgtcattattatttatactcatgcaaaa---
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------------GTGAAGTTTTCAGCTGAAGAGCTTCGTGCCATTATGGACAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagt--ggattccacctccttagctcaatgccatcgaattatttcgttctaggtcttgcgctcgtgaggt-ataatatatctctcctataaggtgaattgt
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S431_2V6.1 (Physcomitrella patens), 5'ss of exon 2
TCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttgagtag--agtgctctaagactgttatacaactattatctttttcctgat-atgccacctg-ttatgttgtcattattatt-tatactcatgcaaaa
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------------GTGAAGTTTTCAGCTGAGGAGCTCCGTGCTATTATGGACAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatcagaaactattacttagtggatttcctatgattactattctgacacaattgacttcatcgaattgaatttcgaaagttactctgtgttcaag-----
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ28367 (Selaginella moellendorffii), 5'ss of exon 2
TCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttgagtagagtgctctaagactgttatacaactatta-tctttttcctgatatgc-cacctgttatgttgtcattattatttatactcatgcaaaa
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------------GTGAAATTCACGGCAGAAGAGCTGCGCCGGATCATGGACAAGAAGCACAACATCCGGAACATGTCTGTGATTGCTCATGTCGATCACGgtgagtttcttctagattttcca--tccattcagtagctaaagctcgtcgatctgaaattttcgccag----------------------------------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|86888335|gb|CI303617.1|CI303617EST: CAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATG GAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCC
genomic: CAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttga ... ttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCACTCACAATGGTTAAGTTTACGGTTGAAGAGATGCGCAGGATTATGGACAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttgagtagagtgctctaagactgttatacaactattatctttttcctgatatgccacctgttatgttgtcattattatttatactcatgcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC