Sequence
atgc intronic sequence ATGC exonic sequence...ggattgttgaggactcctaaaatgttccctcacatgctctatacacattttttctattctgtgatggtctatatgattttgggaaattgtgatgttttagAGAACATCGGACATGGAGTTCTTTACGGAATACGGGGAGGCAAGCCAATATCAGATTCAAGAGGTCGTTGGCAAGGGAAGCTATGGAGTAGTTGCTGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g04230.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g04230.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G374088_T01 (Zea mays), 3'ss of exon 1
ggattgttgaggactcctaaaatgttccctcacatgctctatacacattttttctattctgtgatggtctatatgattttggg-aaattgtgatgttttagAGAACATCGGACATGGAGTTCTTTACGGAATACGGGGAGGCAAGCCAATATCAGATTCAAGAGGTCGTTGGCAAGGGAAGCTATGGAGTAGTTGCTGCTG--
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-agttatttcttcagcctagtatgctctctt-tatatgttttcaacttattgcagattcatttttagacataaaaacctagtacaaattatgatgttt-acagAACACTGGACATGGACTTCTTCACGGAATATGGGGAGGCGAGTCAGTATCAAATCCAAGAGGTCATTGGTAAGGGAAGTTATGGAGTAGTTGCTGCTGCA
upper sequence: LOC_Os02g04230.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G01450.1 (Arabidopsis thaliana), 3'ss of exon 1
-------ggattgttgaggactcctaaaatgttccc---tcacatgct--ctatacacattttttctattc-tgtgatggtctatatgattttgggaaattgtgatgttttag-
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gtcttttggatc-tagggttttattatagcatttctgggttctttgttgaccaagaagaagatttgtattgatggaatgttgttgatgttgttgtgaa-cagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAAGCAAGTCAATATCAGATCCAAGAAGTTGTTGGCAAAGGAAGCTACGGAG------------
upper sequence: LOC_Os02g04230.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G01450.2 (Arabidopsis thaliana), 3'ss of exon 1
-----------ggattgttgaggactcctaaaatgttccc---tcacatgct--ctatacacattttttctattc-tgtgatggtctatatgattttgggaaattgtgatgttttag-
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gtttgtcttttggatc-tagggttttattatagcatttctgggttctttgttgaccaagaagaagatttgtattgatggaatgttgttgatgttgttgtgaa-cagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAAGCAAGTCAATATCAGATCCAAGAAGTTGTTGGCAAAGGAAGCTACGGAG------------Mapped 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|88339735|gb|CI647599.1|CI647599EST: GTGGTGGTGGTGGCACAGCAGAACAATTCCTTCAAATTCAGTGGTAGCAA AGAACATCGGACATGGAGTTCTTTACGGAATACGGGGAGGCAAGCCAATAT
genomic: GTGGTGGTGGTGGCACAGCAGAACAATTCCTTCAAATTCAGTGGTAGCAAgtaagaacct ... gatgttttagAGAACATCGGACATGGAGTTCTTTACGGAATACGGGGAGGCAAGCCAATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattttttctattctgtgatggtctatatgattttgggaaattgtgatgttttagAGAACATCGGACATGGAGTTCTTTACGGAATACGGGGAGGCAAGCCAATATCAGATTCAAGAGGTCGTTGGCAAGGGAAGCTATGGAGTAGTTGCTGCTG
tatatgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggattgttgaggactcctaaaatgttccctcacatgctctatacacattttttctattctgtgatggtctatatgattttgggaaattgtgatgttttagAGAACATCGGACATGGAGTTCTTTACGGAATACGGGGAGGCAAGCCAATATCAGATTCAAGAGGTCGTTGGCAAGGGAAGCTATGGAGTAGTTGCTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT