Sequence
atgc intronic sequence ATGC exonic sequence...actaggagctttatctgcttgactgttgtttgtctaaacagacaacatactaatttgttacctagaaatggttataatcttgatccaatatcgtcttcagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTCCCGAGTTCTTCGGTATAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g42950.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g42950.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
actaggagctttatctgcttgactgttgtttgtctaaacagacaacatact-----aatttgttacctagaaatggttataatctt-gatccaatatcgtcttcagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTCCCGAGTTCTTCGGTATAAA
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-----caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggcacaatttggtaccta-aaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
upper sequence: LOC_Os01g42950.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G22870.1 (Arabidopsis thaliana), 3'ss of exon 6
actaggagctttatctgc-ttgactgttgtttgtctaaacagacaacatactaatttgttacctagaaatggttataatcttga------tccaatatcgtcttcagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTCCCGAGTTCTTCGGTATAAA
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----------gtatgtatattaaattttaatcatcgtttcagacag-acgtgattttgatagttggaaacatataaaacctttggggcatttttttatttattgcagGAGAGAGACAACATGCAGAAGTCTGAGTTCTTAAAAGCATTATCAGATATGTGGAAAGACTTTGATTCTCGTGTATTACGGTATAAG
upper sequence: LOC_Os01g42950.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0089g00030.t01 (Vitis vinifera), 3'ss of exon 6
---------------actaggagctttatctgctt--gactgttgtttgtctaaacagacaacatactaatttgttacctagaaa--tggt-----tataatcttgat--ccaatatcgtctt----cagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTCCCGAGTTCTTCGGTATAAA
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gtatgaagttatatttctttggatgtcacctgcttttgacataagattactaaaaaacattgtgcatgagaaggaaaaataagaagttggtggcaatggaatctgagtaacaaattttatttttttgcagGAAAGGGATAACATGCAGAAGTCTGAGTTTCTAAAAGCATTATCGGATATGTGGAAAGATTTTGACTCTCGTGTTTTGCGTTATAAGMapped 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|58665583|gb|CK054269.1|CK054269EST: TCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTGACCATTTGCTT GAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATG
genomic: TCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTGACCATTTGCTTgtatgtgtct ... tcgtcttcagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATG
EST:
gi|29622819|gb|CB627830.1|CB627830EST: TCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTGACCATTTGCTT GAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATG
genomic: TCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTGACCATTTGCTTgtatgtgtct ... tcgtcttcagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catactaatttgttacctagaaatggttataatcttgatccaatatcgtcttcagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTCCCGAGTTCTTCGGTATAAA
tcgtcttc CT-rich tract
taatttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actaggagctttatctgcttgactgttgtttgtctaaacagacaacatactaatttgttacctagaaatggttataatcttgatccaatatcgtcttcagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTCCCGAGTTCTTCGGTATAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG