Sequence
atgc intronic sequence ATGC exonic sequence...gtatataatagatcatttgatgcctttttccgtatctctaacttacacttggaggctgacaaattccattttcattatcctgtttttaacctgggggaagATAGCAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACA
Basic information
species | Oryza sativa |
transcript | LOC_Os10g33275.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 4
gtatataatagatcatttgatgcctttttccgtatctctaa--cttacacttggaggctgacaaattccattttcattatcctg--tttttaacctgggggaagATAGCAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACA----
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-------tttcaccatttgatacctactgttttgcctatgaaccatactcttcaaagctgacaaattctactttacctggtttgcatttttaacgtgggg-aagatagTAATGCATACAACAAAGGGAAGACACTTGTTTTCAGCAAGGTACCCTTACCTGATTATCGAGCAGATCTGGACGACAGGCATGGATCAACACAAAAGGAG
upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 4
--gtatataatagatcatttgatgcctttttccgtatctctaacttacacttggaggctgacaaattccattttcattatcctgtttttaacctgggggaagATAGCAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACA----
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aagcatagattacctgtactgatgaacattttg--agcttaatcttatttttttattttaactaa---catcttaat-ggcttgatttgtacttgggcaaagaaagCCATGCTTATAGTAAGGGGAAGGTTCTCATTGTTAGCAAAGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAAGAG
upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 2
gtatataatagatcatttgat-gcctttttccgtatctctaacttacacttggaggctgacaaattccattttcattatcctgtttttaacctgggggaagATAGCAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACA----
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---tactgcgcatagattagcagtactcatgaacatgttgagctta-atctgattttttataactaacatcttaatggttttatttgta-cttgggcaaagaaagCCATGCTTATAGTAAGGGGAAGGTTCTCGTCATTAGCAAGGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAGGAG
upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatataatagatcatttgatgcctttttccgtatctctaacttacacttggaggctgacaaattccattttcattatcctgtttttaacctgggggaa-gATAGCAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACA----
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-------gtaagtc--tctatatcttcttcgacaacttcgttttaagtccatatggtgagagt-----atgtcatgaatttgcttatcgttttttggaatggaagTCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAGMapped 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|58673306|gb|CK061992.1|CK061992EST: GATGGACAAAACATACTGGCAGATATGGCTCAGAGACAAGGGCTTTACTT ATAGCAATGTGTACAACAAAGGG
genomic: GATGGACAAAACATACTGGCAGATATGGCTCAGAGACAAGGGCTTTACTTgtaagtgtca ... ctgggggaagATAGCAATGTGTACAACAAAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacttggaggctgacaaattccattttcattatcctgtttttaacctgggggaagATAGCAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACA
ttttaac putative branch site (score: 2)
attttcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatataatagatcatttgatgcctttttccgtatctctaacttacacttggaggctgacaaattccattttcattatcctgtttttaacctgggggaagATAGCAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - gctgaca