Sequence
atgc intronic sequence ATGC exonic sequence...cttttgctcctttatttcttcttctatctccttgaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g40510.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
cttttgctcctttatttcttcttctatctcctt----gaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
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gttttcttcatttaagacaaatgcgaactgcgttatgaaatcatagatgttatctctgttcttcatagaaccttttgctt-acacttgtatgtcttt---gcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 2
cttttgctcctttatttcttcttctatctcc----ttgaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
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tttttctttatttaagtcaaatgcgaactgcgatatgaaatcatagatgttatctctgttcttcatagaaccttttgctt-acacttgtatgtcttt---gcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 1
cttttgctcctttatttcttcttctatctccttgaattattttcattataaaatatttaagtgcaccattttttttgaca-----ctaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
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-----gtgtctttatatatctatgaaatgctctcagtgagtgttgatattttatttctaggatttttttttcttctttctattttttcacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGT
upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 1
----cttttgctcctttatttcttcttctatctccttgaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
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cttgatgtgggtagatgatttaggggcttgtctttttatattatttttgttctttttctttcttttattttcttttcttt----tttacatttttattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTMapped 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|58666336|gb|CK055022.1|CK055022EST: GGCCTCCTCGCGGCGCCGCAG ATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTGGATTCAAGTACA
genomic: GGCCTCCTCGCGGCGCCGCAGgtggcccaat ... tttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
cactaat putative branch site (score: 2)
ttattttct CT-rich tract
attttttttgacacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttgctcctttatttcttcttctatctccttgaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
- -ttgctcc
- - - - - - - - - - - - - -ctccttg
- - - - - - - - - - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acactaa