Sequence
atgc intronic sequence ATGC exonic sequence...acgaaggcttaattggtctaaaaacatcaatatctacatgtcactgtgcatacctttcagtttgtgtggcttgtgcaccatttcaactctctcttttcagGGTTTGTGTGAACAAACTGTAAATGTTCTTCAATTGATGGAGGCAGAAGGAATTGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g49670.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g49670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G028108_T02 (Zea mays), 3'ss of exon 1
acgaaggcttaattggtctaaaaacatcaatatctacatgtcactgtgcatacctttcagtttgtgtggcttgtgcaccatttcaactctctcttttcagGGTTTGTGTGAACAAACTGTAAATGTTCTTCAATTGATGGAGGCAGAAGGAATTGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTA---------------------------------
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-----------------------gtttcaatccatgcgaatca---tgttgactgctcactcaaggagt------caaggtgttccctttctcttt-cagggactgtgtgaacaaactgtaaatgtacttcagTTGATGGAGGAAGAAGGATTTGAGCCAAACCTTGTTATGCTGAATTCGTTAATCAATGCTTTTGGCACTGCTGGAAGGCATTTGGAGGCACTAGCTGTAT
upper sequence: LOC_Os06g49670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G028108_T03 (Zea mays), 3'ss of exon 1
acgaaggcttaattggtctaaaaacatcaatatctacatgtcactgtgcatacctttcagtttgtgtggcttgtgc--accatt---tcaa--------------ctctctct-tttcagGGTTTGTGTGAACAAACTGTAAATGTTCTTCAATTGATGGAGGCAGAAGGAATTGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTA
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--------------------agaatgtcgatatctgcctgtccttatgcacatgtttcaatccatgcgaatcatgttgactgctcactcaaggagtcaaggtgttccctttctctttcagGGACTGTGTGAACAAACTGTAAATGTACTTCAGTTGATGGAGGAAGAAGGATTTGAGCCAAACCTTGTTATGCTGAATTCGTTAATCAATGCTTTTGGCA
upper sequence: LOC_Os06g49670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv16s0039g02560.t01 (Vitis vinifera), 3'ss of exon 1
------acgaaggcttaattggtctaaaaacatcaatatctacatgtcactgtgcatacctttcagtttgtgtggcttgtgcaccatttcaactctctctttt----cagGGTTTGTGTGAACAAACTGTAAATGTTCTTCAATTGATGGAGGCAGAAGGAATTGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTA
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atttgctttttgtccaagttgagttaagaggattaac-tctctatttgacca---acatctatgaagat------ttcatgcaacactgtaattgtgatttcttgagcagGGTTTATGTGAGCAAACAGTTAAGGTTCTTCAGCTCATGGAGACAGAAGGAATTGAACCAAACCTTATAATGCTGAACATGTTGATCAATGCATTTGGCAMapped 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|27547470|gb|CA765633.2|CA765633EST: AGCTTT-ACCTAGCATCTTTTGTGTCTTGGCCAATGCATATGCTCAACAG GGTTTGTGTGAACAAACTGTAAATGTTCTTCAATTGATGGAGGCAGAAGGA
genomic: AGCTTTCACCTAGCATCTTTTGTGTCTTGGCCAATGCATATGCTCAACAGgttagtctag ... ctcttttcagGGTTTGTGTGAACAAACTGTAAATGTTCTTCAATTGATGGAGGCAGAAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcatacctttcagtttgtgtggcttgtgcaccatttcaactctctcttttcagGGTTTGTGTGAACAAACTGTAAATGTTCTTCAATTGATGGAGGCAGAAGGAATTGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTA
ccatttcaactctctc CT-rich tract
atttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acgaaggcttaattggtctaaaaacatcaatatctacatgtcactgtgcatacctttcagtttgtgtggcttgtgcaccatttcaactctctcttttcagGGTTTGTGTGAACAAACTGTAAATGTTCTTCAATTGATGGAGGCAGAAGGAATTGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG