Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgaaatgatcattttataatattctaacagtaatgtacattatttaacttattgttcctttgacctccttaatagGGACATCACCTTGCTGAAACCAGAGGTCTCTGCCTATCTGAAGAGCAAATTGTCCGAACT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g42820.4 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g42820.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G342105_T02 (Zea mays), 3'ss of exon 5
gtaagtgaaatgatcattttataatattctaacagtaatgtacattattta-acttattgttcctttgacctccttaatagGGACATCACCTTGCTGAAACCAGAGGTCTCTGCCTATCTGAAGAGCAAATTGTCCGAACT
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gtaagtgaca----ccctttcctttattat----gtggtatatataacatatatctaatgtactctcgtcg-----attagGTGCACCACCTTCCTGAAACAAGAGGCCTCTGCCTATCTGAGGAGCAGATTGTCAGAACT
upper sequence: LOC_Os03g42820.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G869767_T01 (Zea mays), 3'ss of exon 1
gtaagtgaaatgatcattttataatattctaacagtaatgtacattatttaacttattgttcctttgacctccttaat-agGGACATCACCTTGCTGAAACCAGAGGTCTCTGCCTATCTGAAGAGCAAATTGTCCGAACT
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gtaagtgaca----ccctttcctttattgtgtgaata-tgtggtatatataacatatatccaatgtactctcgtcgattagGTGCACCACCTTCCTGAAACAAGAGGCCTCTGCCTATCTGAGGAGCAGATTGTCAGAACT
upper sequence: LOC_Os03g42820.4 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G66640.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtgaaatgatcattttataatattctaacagtaatgtacattat-ttaacttattgttcctttgacctccttaatagGGACATCACCTTGC---TGAAACCAGAGGTCTCTGCCTATCTGAAGAGCAAATTGTCCGAACT
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gtgagt---atatttagaaaacacatccctcatcactttgtaactcatctttgtttctcatatttatgtcaatacaaacagGACTACCATCGTGCAGCCGTAACCAGAGGTCTTTGCATGTCTGAAGAGCAAATTGTCCCAAGT
upper sequence: LOC_Os03g42820.4 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G66620.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagtgaaatgatcattttataatattctaacagtaatgtacattatttaacttattgttcctttgacctccttaatagGGAC-ATCACCTTG---CTGAAACCAGAGGTCTCTGCCTATCTGAAGAGCAAATTGTCCGAACT
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gtgagtacattagttatttgaaacttccatctttctctctctctctcactcatatgttttataaaaaatttacacaagcagGACTATCAGTATGAGGTGGTAACCAGAGGTATTTGCCTATCTGAAGAGCAGATTGTCGATAGTMapped 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|2311882|gb|C28037.1|C28037EST: TGTTGGTTGAGCGACAAG-TTTAAATGAAGCCATGGAGGCCGAGAAAACT GGACATCACCTTNCTTGAAACCAGAGG
genomic: TGTTGGTTGAGCGACAAGCTTTAAATGAAGCCATGGAGGCCGAGAAAACTgtaagtgaaa ... tccttaatagGGACATCACCTTGCT-GAAACCAGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctaacagtaatgtacattatttaacttattgttcctttgacctccttaatagGGACATCACCTTGCTGAAACCAGAGGTCTCTGCCTATCTGAAGAGCAAATTGTCCGAACT
ttcctttgacctcctt CT-rich tract
taatgtacattattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgaaatgatcattttataatattctaacagtaatgtacattatttaacttattgttcctttgacctccttaatagGGACATCACCTTGCTGAAACCAGAGGTCTCTGCCTATCTGAAGAGCAAATTGTCCGAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA