Sequence
atgc intronic sequence ATGC exonic sequence...aattttaataccagatatagcaaggattgcttgcaaggttgagctatgcatttgagatttatttgctgattgtagtaacaaaatcttacgattggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g58114.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G139374_T02 (Zea mays), 3'ss of exon 4
aattttaataccagatatagcaaggattgcttgcaaggttgagctatgcatt-tgagatttatttgctgattgtagtaacaaaatctt-acgattggcc-tagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
||| || |||| | | | | || ||||| | |||||| | || | ||| | | | || ||||||| | || || || ||||||| ||||| |||||| | |||| ||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||
ggtttctattccagtttttcttttaacagttt---aggtttgattctgcattgtttgaatggtttattagctttgttactgaaatctttatgaatgtccacagGTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G45930.1 (Glycine max), 3'ss of exon 4
aattttaataccagatatagcaaggattgcttgcaaggttgagctatgca-tttgagatttatttgctgattgtagtaacaaaatcttacgattggcct--agGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
| | | || | | | || | |||| | || | || | || | | | | | ||| || ||||||| | || ||||| || |||| |||||||||| || ||||| || || |||||||| |||||| | |||||||| |||||||||||
---tcttctgccctttccgtcttttttatgttttagccacatgctacatagcttaatgctttatgaacgagtctttttgagcatttactttgttgctctgcagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAA
upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G02820.1 (Glycine max), 3'ss of exon 4
aattttaataccagatatagcaaggattgcttgcaaggttgagctatgcatttgagatttatttgctgattgtagtaacaaaatcttacgattggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
| || | | | | || || | | || ||| | | | | | || | || | | || ||| ||||||| | || ||||| || |||| |||||||||| || ||||| || || |||||||| |||||| | |||||||| |||||||||||
ttctctatcttctgccctttctgtctttttttttatgttttagccacatgctacatagcttaatgttttatgaatgagcatttactttgttgctctgcagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAA
upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G27020.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------aattttaataccagatatagcaaggattgcttgcaaggttgagctatgcatttgagatt-tatttgctgattgtagtaacaaaatcttacg-attggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
|| | | | | || || | | ||| | || ||| |||| | || ||| | | | | ||| || | ||||||| ||||| ||||| | |||| |||| | || || || |||||||| ||||||||||| |||||||||||||| || || ||||| ||
gtaggttttcatttctcagaattttggcattgatgacaacataagtttcagtttatctctttattgttctctctttaatcagcttctatcagttagtttatgggtgaggttgtgattgttttctctgtatctcttttccttctctattatgtttttccagGTTGCTTCTGTCATGACAGTTTGGAGCAAAATCCAGCCTGATTATGCTGCTAACATGTGGAATGAAGCCCTTAACAAGCGACTCGGAACAGAG
upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ34102 (Selaginella moellendorffii), 3'ss of exon 4
aattttaataccagatatagcaaggattgcttgcaaggttgagctatgcatttgagatttatttgctgattgtagtaacaaaatcttacgattggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
| || || || ||| | | | | | | | || || |||| ||||| || || ||| | || | |||| ||| |||||||||||||||||||| |||||||| ||||| || ||||| || || | ||| ||
-----------------------------------------gtaagagagctttagtttcctttccaaagcttgttgatacatgttttcggttgggatagGTGGCTTCGGTGCTCACGGTCTGGACTCGACTCCAACCAGAGTATGCTGCCAATATGTGGAATGAAGCTCTCAACAAGCGTCTCGACACTCAG
upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ12449 (Selaginella moellendorffii), 3'ss of exon 4
aattttaataccagatatagcaaggattgcttgcaaggttgagctatgcatttgagattta-tttgctgattgtagtaacaaaatcttacgattggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
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-----------------------------------------------gtaagagagctttagtttccaaagcttgttgacacattttctcggttgggatagGTGGCTTCGGTGCTCACGGTCTGGACTCGACTCCAACCAGAGTATGCTGCCAATATGTGGAATGAAGCTCTCAACAAGCGTCTCGACACTCAGMapped 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|3107375|gb|D43115.1|D43115EST: GGATTGATACCATAAGCGACAACTATCCACCGCCATTAGATGCTCATGTG GTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCC
genomic: GGATTGATACCATAAGCGACAACTATCCACCGCCATTAGATGCTCATGTGgtatgatcaa ... attggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCC
EST:
gi|218493202|gb|FG958053.1|FG958053EST: GGATTGATACCATAAGCGACAACTATCCACCGCCATTAGATGCTCATGTG GTTGCCTCTGTTATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCC
genomic: GGATTGATACCATAAGCGACAACTATCCACCGCCATTAGATGCTCATGTGgtatgatcaa ... attggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCC
EST:
gi|25797971|gb|CA753932.1|CA753932EST: GGATTGATACCATAAGCGACNACTATCCACCGCCATTAGATGCTCATGTG GNTGCCTCTGTGATGACTATGTGGGACAAACTTCAACCAGAGTATGCTGCC
genomic: GGATTGATACCATAAGCGACAACTATCCACCGCCATTAGATGCTCATGTGgtatgatcaa ... attggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
38 (upstream exon),
75 (downstream exon)
Score:
9AAAAAGCATGGATGGAAAACCTTATGGGTACCACAATATGATTTTTAGTTGGATTGATACCATAAGCGACAACTATCCACCGCCATTAGATGCTCATGTGgtatgatcaa ... attggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcatttgagatttatttgctgattgtagtaacaaaatcttacgattggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
tttgagatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattttaataccagatatagcaaggattgcttgcaaggttgagctatgcatttgagatttatttgctgattgtagtaacaaaatcttacgattggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - -tgcttgc
- - - - - - - - - - - - - - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taacaaa