Sequence
atgc intronic sequence ATGC exonic sequencegtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaatgatgagacatgaactctacttttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23610.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
--------gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaat--gatgagacatgaactctact--tttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
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gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgc--------------acggagaattc---cagtggatacattaaccagacctatgctagggagc--ctgtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaatgatgagacatgaactctacttttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
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-----------------------------------------------tcttgaccgtattc-actcttatgctt--ttctctaggtgcattgttgtt------gttctttacttgtctcattgtttactaactatttttaagctgt---tttcatgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaatgatgagacatgaactctacttttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
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---------------------------------------------cttcttgaccgtatttaactcttaccttt--ttctctagttgcattgctgttctttacttgctttattgttt---------actaactacttttaagctgt---tttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaatgatgagacat--gaactctacttttgct---acagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
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----------------------------------------------------------gtgaagagaagaaccaaaaattgaaataaaa--aaagatagttgtatatagttctggagtgacttgcgaa-gataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 12
gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaact-tgaaaatgatgagacatgaactctacttttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
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---------------------------------------------------------attagaaagt-gcttttagc-ccattttaaaattactcccaaataagctcttagtctttctacttctgccatttgccaattcttctgtctattttcatc-cagTTGATATACAGACCTGACAATGGAGAGATTCTTGGAGTGCACATCTTTGGGTTGCATGCTGCAGACCTTATCCATGAAGCATCCAATGCTATAGCACTAGMapped 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|218481788|gb|FG954747.1|FG954747EST: AGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAGATGGACTTGCTAAG ATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGT
genomic: AGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAGATGGACTTGCTAAGgtgattctac ... tttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGT
EST:
gi|33678411|gb|CF306650.1|CF306650EST: CTGAGAATGAAGGAGATGGACTTGCTAAG ATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGT
genomic: CTGAGAATGAAGGAGATGGACTTGCTAAGgtgattctac ... tttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatctatccttggaacttgaaaatgatgagacatgaactctacttttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
ctctactttt CT-rich tract
ttgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaatgatgagacatgaactctacttttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT