Sequence
atgc intronic sequence ATGC exonic sequencegtatgatacttgatataatggtattttgtttttgtggaaccacatgttgctcttagttctaatctatgaaacatcacttttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACTTGCTGATTTTGGGATGGCCAAGCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g10100.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 5
gtatgatacttgatataatggtattttgtttttgtggaaccacatgttgctcttagttctaatctatgaa-acatcacttttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACTTGCTGATTTTGGGATGGCCAAGCAT
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gtattttgattattcctacgcaatctt--taacgtggcatttagtcttatttattctttcatattgtcatcgtggttttcttttggcagGGATATTAAAGGGGCGAACATACTAGTTGATCCTAATGGTGAAATCAAACTGGCAGACTTTGGAATGGCTAAACAT
upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G15870.1 (Glycine max), 3'ss of exon 6
gtatgatacttgatataatggtattttgtttttgtggaacc---acatgttg-ctcttagttctaatctatgaaacatcacttttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACTTGCTGATTTTGGGATGGCCAAGCAT
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gtaatttaaatggc-tactcaagatttatttatgttaaatgcaagcatcttgactctttattatagtat-tgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G16670.2 (Glycine max), 3'ss of exon 5
gtatgatacttgatataatggtattttgtttttgtggaacc---acatgttgctcttagttctaatctatgaaacatcacttttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACTTGCTGATTTTGGGATGGCCAAGCAT
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gtattttgattattcctacgcaatctt--taacatgaaatttaggcttatttattctctttcatattgttatcgtggttttcttttggcagGGATATTAAAGGGGCGAACATACTAGTTGATCCTAATGGTGAAATCAAACTGGCAGACTTTGGAATGGCTAAACAT
upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 5
----gtatgatacttgatataatggtattt-tgtttttgtggaaccacatgttg-ctcttagttctaatctatgaaacatcacttttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACTTGCTGATTTTGGGATGGCCAAGCAT
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gtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtat-tgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACATMapped 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|109974299|gb|DT806830.1|DT806830EST: CAAATTCTTTCTGGCCTTGCATATTTGCATGGGCGGAATACAGTGCATAG GGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACT
genomic: CAAATTCTTTCTGGCCTTGCATATTTGCATGGGCGGAATACAGTGCATAGgtatgatact ... tttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACT
EST:
gi|29680776|gb|CB677051.1|CB677051EST: CAAATTCTTTCTGGCCTTGCATATTTGCATGGGCGGAATACAGTGCATAG GGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACT
genomic: CAAATTCTTTCTGGCCTTGCATATTTGCATGGGCGGAATACAGTGCATAGgtatgatact ... tttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggaaccacatgttgctcttagttctaatctatgaaacatcacttttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACTTGCTGATTTTGGGATGGCCAAGCAT
ttctaat putative branch site (score: 2)
tcacttttctc putative PPT
taatctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatacttgatataatggtattttgtttttgtggaaccacatgttgctcttagttctaatctatgaaacatcacttttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACTTGCTGATTTTGGGATGGCCAAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT