Sequence
atgc intronic sequence ATGC exonic sequencegtaagatgttgaaactaacatcctcttttcattgatgcaagtatcacgccatttagtgatagtaacttcgctgaaagtgtgggatgagctagccattgcttccattttgtgcatggtttatgttgaaacgggaaatgtgatgctgtcctttgcgcctgtgtgcagTCGTTCCTCTACCAGATTCTCCGGGGCATTGCGTACTGCCACTCGCACCGTGTTCTCCACCGAGATTTGAAGCCCCAGAACCTGCTGATAGATCGGCGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g03060.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g03060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G174596_T02 (Zea mays), 3'ss of exon 3
gtaagatgttgaaactaacatcctcttttcattgatgcaagtatcacgccatttagtgatagtaacttcgctgaaagtgtgggatgagctagccattgcttccattttgtgcatggtttatgttgaaacgggaaatgtgatgctgtcctttgcgcctgtgtgcagTCGTTCCTCTACCAGATTCTCCGGGGCATTGCGTACTGCCACTCGCACCGTGTTCTCCACCGAGATTTGAAGCCCCAGAACCTGCTGATAGATCGGCGTA
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---------------------------------------------------------------------gtcagcctctcctcctccacggactgtgaatcgtagtagttgtgagatatgaactgcaaattgtaatgccacgctatgctcccctgtgccgtgcagTCCTTCCTCTACCAGATTCTGCGGGGCATCGCCTACTGCCACTCGCACCGCGTGCTCCACCGCGACCTGAAGCCGCAGAACCTGCTGATTGACCGCCGCA
upper sequence: LOC_Os02g03060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagatgttgaaactaacatcctcttttcattgatgcaagtatcacgccatttagtgatagtaacttcgctgaaagtg-tgggatgagctagccattgcttccattttgtgcatggttt--atgttgaa-acgggaaatgtgatgctgtcctttgcgcctgtgtgcagTCGTTCCTCTACCAGATTCTCCGGGGCATTGCGTACTGCCACTCGCACCGTGTTCTCCACCGAGATTTGAAGCCCCAGAACCTGCTGATAGATCGGCGTA
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------------------------------------------------------------------------gtgagtgctaagaaactttaggcattgttttatatatgtgcttaaactcaatactcaatataagctgatcagagctgttcat--ccactattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA
upper sequence: LOC_Os02g03060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
gtaagatgttgaaactaacatcctcttttcattgatgcaagtatcacgccatttagtgatagtaacttcgctgaaagtgtgggatgagctagccattgcttccattttgtgcatggtttatgttgaaacgggaaatgtgatgctgtcctttgcgcctgtgtgcagTCGTTCCTCTACCAGATTCTCCGGGGCATTGCGTACTGCCACTCGCACCGTGTTCTCCACCGAGATTTGAAGCCCCAGAACCTGCTGATAGATCGGCGTA
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----------------------------------------------------------------tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggtgcgatggggcttctgacacttgagtcc-tttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatggtttatgttgaaacgggaaatgtgatgctgtcctttgcgcctgtgtgcagTCGTTCCTCTACCAGATTCTCCGGGGCATTGCGTACTGCCACTCGCACCGTGTTCTCCACCGAGATTTGAAGCCCCAGAACCTGCTGATAGATCGGCGTA
tttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatgttgaaactaacatcctcttttcattgatgcaagtatcacgccatttagtgatagtaacttcgctgaaagtgtgggatgagctagccattgcttccattttgtgcatggtttatgttgaaacgggaaatgtgatgctgtcctttgcgcctgtgtgcagTCGTTCCTCTACCAGATTCTCCGGGGCATTGCGTACTGCCACTCGCACCGTGTTCTCCACCGAGATTTGAAGCCCCAGAACCTGCTGATAGATCGGCGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT