Sequence
atgc intronic sequence ATGC exonic sequencegtgcaaaattgcaattattatattatatatacttgttctctgttagttttctaatcatggagtgctttatccagCAAAGTGCAAGTCGAGAACCCTGCAGCTTTGGCTTCAAATCCTGGAAAGCGTATAGCAGCTTGTTGGGAACCAACAGTCATTGCAACTATTATTATTCCT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05250.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05250.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G028928_T02 (Zea mays), 3'ss of exon 4
gtgcaaaattgcaattattatattatatatacttgttctctgttagttttctaa----tcatggagtgctttatccagCAAAGTGCAAGTCGAGAACCCTGCAGCTTTGGCTTCAAATCCTGGAAAGCGTATAGCAGCTTGTTGGGAACCAACAGTCATTGCAACTATTATTATTCCT
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gtctgcactcac---tattgtatttgctacctcggttttctggtaggatactaaaactttttaggttatttttatcagCAAGGTGCAAGTTGAGAACCCTGCTGCTTTGGCTTCGAATCCTGGAAAGCGTGTAGCAGCCTGTTGGGAGCCCACAGTTATTGCAACAATCATTATTCCT
upper sequence: LOC_Os06g05250.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0108g00130.t01 (Vitis vinifera), 3'ss of exon 5
--gtgcaaaat-tgcaattattatattatatatacttg-ttctctgttagttttctaat----catggagtgct---ttatccagCAAAGTGCAAGTCGAGAACCCTGCAGCTTTGGCTTCAAATCCTGGAAAGCGTATAGCAGCTTGTTGGGAACCAACAGTCATTGCAACTATTATTATTCCT
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gtatgtagcatatttggtcatttctcttta-atgctaggttccacattttttttaccatataatatgtattggtctcttgtttagCAAAATACAGGTCCAGAATCCTGCTGCATTAGCTTCAAATCCCGGTAAACGAGTAACAGCTTGTTGGGAACCTACAGTGATAGCTACAATTATTATTCCTMapped 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|58693249|gb|CK081936.1|CK081936EST: ATATCGACAATACCGACAGTGCCATATATCTTTGAGTATGGTGATGGAAG CACAGTGCAAGTCGAGAACCCTGCAGCTTTGGCTTCCAATCCTGGAAAGCG
genomic: ATATCGACAATACCGACAGTGCCATATATCTTTGAGTATGGTGATGGAAGgtgcaaaatt ... ctttatccagCAAAGTGCAAGTCGAGAACCCTGCAGCTTTGGCTTCAAATCCTGGAAAGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattatatatacttgttctctgttagttttctaatcatggagtgctttatccagCAAAGTGCAAGTCGAGAACCCTGCAGCTTTGGCTTCAAATCCTGGAAAGCGTATAGCAGCTTGTTGGGAACCAACAGTCATTGCAACTATTATTATTCCT
ttctaat putative branch site (score: 2)
ctttatcc putative PPT
atatatactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcaaaattgcaattattatattatatatacttgttctctgttagttttctaatcatggagtgctttatccagCAAAGTGCAAGTCGAGAACCCTGCAGCTTTGGCTTCAAATCCTGGAAAGCGTATAGCAGCTTGTTGGGAACCAACAGTCATTGCAACTATTATTATTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT