Sequence
atgc intronic sequence ATGC exonic sequencegtttgtggattaggaacttactatatctagcttatctggtttatacttatttagttgacatgggtcagtaatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g36960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 4
-gtttgtggattaggaacttactat-atctagcttatctggtttatacttatttagttgacatgggtcagtaatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
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gttttgtagttcaggaacttgttcttaccttgtttcttctgtttgaacttatttagttgaca-aggtgagttatgcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 3
-------------------------------gtttgtggattaggaacttactatatc--tagcttatctggtttatacttatttagttga-catgggtcagt---aatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
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gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------------gtttgtggattaggaacttactatatctagcttatctggtttatacttatttagttgacatgggtcagtaatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
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gtgaagacccttaaaatttttgtataatgtaatcatagacttagtttctttcagttaattgttaatagttacagtattgcaatctctg--ttgtgaactagaagtgtg-agaataatgactgtttacttttctgctaagcacattctactgttgcagGGTTGCTATGTCTGCATTGTCACCGGATACTGTGAAGGTGGAGACAT
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
-----gtttgtgg-attaggaacttactatatctagctta--tctggtttatacttatttagttgacatgggtc--agtaatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
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gtaagttttacatcactttgatttttatggatttaaagtagatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 3
------------gtttgtggattaggaacttactatatc-tagcttatctggt-ttatacttatttagttgacatgggtcagtaatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
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gtaggtcctggaaattctagttttttgacgaatttttttgctgtaaatgcgaccttgtactgaatcgagagctttgggttgg-aatgcagGGTTGCTATGTTTGCATTGTCACTGGATATTGTGAAGGAGGAGACATMapped 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|88402749|gb|CI613197.1|CI613197EST: GGTTGCCACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAG GGTTGCTATGTCTGCATTGTCACG
genomic: GGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgtttgtggat ... agtaatgcagGGTTGCTATGTCTGCATTGTCACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatctagcttatctggtttatacttatttagttgacatgggtcagtaatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
agttgac putative branch site (score: 4)
tttatacttatttagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtggattaggaacttactatatctagcttatctggtttatacttatttagttgacatgggtcagtaatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT