Sequence
atgc intronic sequence ATGC exonic sequencegtatgttctaatcgatttcttgtctgatgttgatgtgaattatggcgttatttttttgggtgatttatggtttgtttgattgcgaacagCGCTCTTGCCGTCGTGGACGATGACGACGGCGGCGACCACCGAGAGGAGCTGAGAGGCGTGCTGCGGCTGTTCCCGATATGGGCGACGTGCATCATCTAC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g65100.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g65100.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G400602_T01 (Zea mays), 3'ss of exon 3
---------gtatgttctaatcgatttcttgtct--gatgttgatgtgaattatggcgttatttttttgggtgatttatggtttgtttgattgc-----gaacagCGCTCTTGCCGTCGTGGACGATGACGACGGCGGCGACCACCGAGAGGAGCTGAGAGGCGTGCTGCGGCTGTTCCCGATATGGGCGACGTGCATCATCTAC------------
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gtaatttctatgtgttttcgtccttgtttggttctcgaggtcgacgcacacca--gtgtaacagtgttagttagtctatacagtgaaagaaaaccgtttgatcatca-tcttggcagCACTCTTGCGAGCGACGACGCCGGGCACCGTGAAGAAGTGAAAGGCGTGCTGCGCCTGTTCCCCATCTGGGCGACGTGCATCATCTACGCCGTCATCTTCMapped 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|29660278|gb|CB656553.1|CB656553EST: GCTCGCCTCGCCAGAGCGTTCGTCGCGCTCATCAGAGGATCCAAAGACGA CGCTCTTGCCGTCGTGGACGATGACGACGGCGGCGACCACCGAGAGGAGCT
genomic: GCTCGCCTCGCCAGAGCGTTCGTCGCGCTCATCAGAGGATCCAAAGACGAgtatgttcta ... ttgcgaacagCGCTCTTGCCGTCGTGGACGATGACGACGGCGGCGACCACCGAGAGGAGCT
EST:
gi|58691589|gb|CK080276.1|CK080276EST: GCTCGCCTCGCCAGAGCGTTCGTCGCGCTCATCAGAGGATCCAAAGACGA CGCTCTTGCCGTCGTGGACGATGACGACGGCGGCGACCACCGAGAGGAGCT
genomic: GCTCGCCTCGCCAGAGCGTTCGTCGCGCTCATCAGAGGATCCAAAGACGAgtatgttcta ... ttgcgaacagCGCTCTTGCCGTCGTGGACGATGACGACGGCGGCGACCACCGAGAGGAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaattatggcgttatttttttgggtgatttatggtttgtttgattgcgaacagCGCTCTTGCCGTCGTGGACGATGACGACGGCGGCGACCACCGAGAGGAGCTGAGAGGCGTGCTGCGGCTGTTCCCGATATGGGCGACGTGCATCATCTAC
gtttgat putative branch site (score: 5)
ttattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttctaatcgatttcttgtctgatgttgatgtgaattatggcgttatttttttgggtgatttatggtttgtttgattgcgaacagCGCTCTTGCCGTCGTGGACGATGACGACGGCGGCGACCACCGAGAGGAGCTGAGAGGCGTGCTGCGGCTGTTCCCGATATGGGCGACGTGCATCATCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT