Sequence
atgc intronic sequence ATGC exonic sequencegtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggcttagttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 14
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggctta--gttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
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-----------------------------------------------------------gtcata-atgcaatctctat---tttaagccctgttgcgtcgctcattaactatcagggcctgcgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 9
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggctta--gttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
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-----------------------------------------------------------gtcata-atgcaatctctat---tttaagccccgttgcatcgcgcattaactatcagggcctgcgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAGCAATCATACAAGGTTAGTGAGTCGTTTCCTTACAAGTGGATTAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 14
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggcttagt-tgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
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-------------------------------------------------------------tgtcc-tatgcaatttccattttaagccccgtttgcatcgctcattaattatcatggtctgctatgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 10
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggctta--gttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
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-----------------------------------------------------------gtcata-atgcaatctctat---tttaagcctcgttgcatcgcgcattaactatcagggcctacgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAGCAATCATACAAGGTTAGTGAGTCGTTTCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 14
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggcttagttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
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---------------------------------------------------tattttagctcgtt--taacttctgtgatgaaaggaacatca-actgttcttcagaattta---tgactt---tatatttatctcatgtttgaatcctttact-ttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCAAATGGATAAACAAGAAGTGGAAAGAAGGATTCCATGTTACCTCAATGAC
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggcttagttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
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-------------------------------------------------------gtcggtagtc---acgtctcatgataactttgccaatgaact------tattgattcataaagcatgaaagccgttttacttattccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtt-tcatatggacttaatcattttgttgctccccatgagttaacctggcttagttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
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------------------------------------------------------tcagtctcatccaaatttgatcatg-gaatttaatcttgtcatgttgcatattgttttgagttggccca--tgtgttta--tatggtgttttctgt---ttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGACMapped 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|218490208|gb|FG966190.1|FG966190EST: AGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG GAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCA
genomic: AGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAGgtctgggatg ... attattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagttaacctggcttagttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
tatagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggcttagttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
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