Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatttaaagtcacttgtgcctgaaaattatatggagctgcatggaatttctcttttgttttctatttcattggtgttaacatttccagtgcatcttatcattgccagGTTTGTACATGGTGATGTCAAACCAGAGAATTTTTTGCTTGGTCATCCTGGGTCAGTTGATGAGAAGAAGCTTTTCCTGATTGATCTTGGTTTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g57940.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g57940.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
gtaaaatttaaagtcacttgtgcctgaaaattatatggagctgcatggaatttctcttttgttttctatttcattggt--gttaacattt-ccagtgcatct--tatcattg--ccagGTTTGTACATGGTGATGTCAAACCAGAGAATTTTTTGCTTGGTCATCCTGGGTCAGTTGATGAGAAGAAGCTTTTCCTGATTGATCTTGGTTTAG
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gtaaacccttgtgatagttttttc----aatcctgtcaacct--ttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
upper sequence: LOC_Os03g57940.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------gtaaaatttaaagtcacttgtgcctga--aaattatatggagctgcatggaatttctcttttgttttctatttcattggtgttaacatttccagtgcatcttatcattgccagGTTTGTACATGGTGATGTCAAACCAGAGAATTTTTTGCTTGGTCATCCTGGGTCAGTTGATGAGAAGAAGCTTTTCCTGATTGATCTTGGTTTAG
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gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcat--gcattgttcattccctacatcaa-acaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
upper sequence: LOC_Os03g57940.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 7
----gtaaaatttaaagtcacttgtgcc------tgaaaattatatggagctgcatgga-atttctcttttgttttctatttcattggtgttaac-atttccagtgcatcttatcattgcc--agGTTTGTACATGGTGATGTCAAACCAGAGAATTTTTTGCTTGGTCATCCTGGGTCAGTTGATGAGAAGAAGCTTTTCCTGATTGATCTTGGTTTAG
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gtgagtactattaataattccatgtttcactttctcagaatcatcctgtctctcttgagcactttcctcaaagtggcttcttcattc-tgttaattattgtcatcttttttcttcctcaaccaagGTTTGTGCATGGAGATGTGAAGCCAGAGAACTTTTTACTTGGTCAACCTGGAACTGCTGATGAGAAGAAGCTATTTCTTATTGATCTTGGTTTGGMapped 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|58609402|gb|CK037435.1|CK037435EST: TGCATTGCTGTGGAAGCGATATCAATTCTTGAGAAGCTTCACTCTAAAGG GTTTGTACATGGTGA
genomic: TGCATTGCTGTGGAAGCGATATCAATTCTTGAGAAGCTTCACTCTAAAGGgtaaaattta ... tcattgccagGTTTGTACATGGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttttctatttcattggtgttaacatttccagtgcatcttatcattgccagGTTTGTACATGGTGATGTCAAACCAGAGAATTTTTTGCTTGGTCATCCTGGGTCAGTTGATGAGAAGAAGCTTTTCCTGATTGATCTTGGTTTAG
tgttaac putative branch site (score: 2)
tcttatc putative PPT
ttttctatttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatttaaagtcacttgtgcctgaaaattatatggagctgcatggaatttctcttttgttttctatttcattggtgttaacatttccagtgcatcttatcattgccagGTTTGTACATGGTGATGTCAAACCAGAGAATTTTTTGCTTGGTCATCCTGGGTCAGTTGATGAGAAGAAGCTTTTCCTGATTGATCTTGGTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC