Sequence
atgc intronic sequence ATGC exonic sequencegtgagtggttatggttttgcagtggtgaatattattttatgagcccaaattttatctgtgtaaatgcaattattttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g14810.2 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g14810.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
gtgagtggttatggttttgcagtggtgaatattatt-ttatgagcccaaattttatctgtgtaaatgcaatta-ttttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG
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gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaact---------gaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
upper sequence: LOC_Os01g14810.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 15
gtgagtggtt--atggttttgcagtggtgaatattattt-tatgagcccaaattttatctgtgtaaatgcaattattttg--tcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG
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gtatgtggtttagtggttacttattgatgaccctgatctctattttatcacattactcttttgatactg-aactgtttaaatttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG
upper sequence: LOC_Os01g14810.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 15
gtgagtggttatggttttgcagtggtgaatattattttatgagcccaaattttatctgtgtaaatgcaattattttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG
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gtatgtgcttacttttttatgaccctgatctctattttatcacattactcttttgatattgaactgtttaaattttattat---tgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG
upper sequence: LOC_Os01g14810.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 15
----------------------gtgagtggttatggttttgcagtggtgaatattattttatgagcccaaa-ttttatctgtgta-aatgcaattattttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG
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gtatgtgcttttccttcattatgccttctttttttcttatgtaggagtaactaa-acttcataaactaagggttctacctttatatgatccttacaatatcttccaattgcagGTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAGMapped 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|86478388|gb|CI121021.1|CI121021EST: TCACGTACGGGCCTATGGGATAAGAGTCATCTGACGAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCC
genomic: TCACGTACGGGCCTATGGGATAAGAGTCATCTGACGAGGCAAATTGAAAAgtgagtggtt ... ctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCC
EST:
gi|86886647|gb|CI312532.1|CI312532EST: TCACGTACGGGCCTATGGGATAAGAGTCATCTGACGAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCC
genomic: TCACGTACGGGCCTATGGGATAAGAGTCATCTGACGAGGCAAATTGAAAAgtgagtggtt ... ctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatgagcccaaattttatctgtgtaaatgcaattattttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG
ttttgtcctc CT-rich tract
taaatgcaattatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtggttatggttttgcagtggtgaatattattttatgagcccaaattttatctgtgtaaatgcaattattttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC