Sequence
atgc intronic sequence ATGC exonic sequencegtatgccacaagcttggaattagttgatcgaatctgaatgatactttcttggctctcatctcaccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g57350.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------gtatgccacaagcttggaattagttg-atcga-atctgaatgatactttcttggctctcatctcaccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
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gtaattataaattactgtcaccatagtcgtgttttggaaacgagtgaatgtgaaaaagcatctaagttacttgtgtcagcatctggttctggccatgatattcgccgtaacat-atttgaaaattttaat--tttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT
upper sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G31980.1 (Glycine max), 3'ss of exon 7
gtatgccacaagcttggaattagttgatcgaatctgaatgatactttcttggctctcatctcaccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
|| || | ||||||| | ||||||| ||||| || ||||||||||| |||||| |||||||||||||||| | | ||||| |||
----------------------------------------------------------------------------gtattattctatttcagatctggtggcagATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTTGGCTAGATTTTTAT
upper sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G07340.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------------------------------gtatgccacaagcttggaattagttgatc---gaatctga--atgatactttcttggc-tctcatctcaccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
| | || |||| |||| ||||| ||| | | |||| | | | || | | || | | || || | ||||||||| ||||||| ||||| || ||||||||||| |||||| |||||||||||||||| || | ||||| |||
gtaattactctcaccatgtactagaaatgaagtggtggcagatgtgctaaaacatctaggctaactgttcgcaattttttctttctcttcttgatttatccagacttaggtgattcttagttctgaccatgcaattgacttgacatattatatgat-atccattggaggtattattttatttcagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTCGTCTAGATTTTTAT
upper sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G21540.3 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------gtatgccacaagcttggaattagttgatcgaatctgaatgata------ctttcttggctctcatctca-ccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
||| | | || | | | || || | ||| | | | ||| || | | | | | | || || | | ||||||||||| |||||||||||||| || ||||| ||||| | ||| |||||||
gtatgcaaggacttctacttctttgtagtgtagtactctagaatgtagaacttgatttg-caaatgcaagtagtggctgagcttactgaattattctgttggttgtactgagagaaattcattttatttcagGTTTAGTGGCTGATATAGACATCGAGTCAGAGAAATTCAGATGGATGG-----------------------
upper sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G21540.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------gtatgccacaagcttggaattagttgatcgaatctgaatgata------ctttcttggctctcatctca-ccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
||| | | || | | | || || | ||| | | | ||| || | | | | | | || || | | ||||||||||| |||||||||||||| || ||||| ||||| | ||| |||||||| ||||| ||||||||| |||||
gtatgcaaggacttctacttctttgtagtgtagtactctagaatgtagaacttgatttg-caaatgcaagtagtggctgagcttactgaattattctgttggttgtactgagagaaattcattttatttcagGTTTAGTGGCTGATATAGACATCGAGTCAGAGAAATTCAGATGGATGGGTAGTGCTCGCTTTGATATCTAT
upper sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G21534.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------gtatgccacaagcttggaattagttgatcgaatctgaatgatactttcttggct--ctcatctcaccattta--gggataataa--taatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
|||| | || | ||| |||| | | | |||| || | | ||| || | | || ||| | | || | || ||||||||||| | ||||||||||| || ||||| ||||||| ||| |||||||||||||| || |||| || |||
gtatgccagtaaattctacttctttttgctatgtccagagttcagaa--agttatttgcaaatgaa-agtaatacatgagcttgctgaacgtactctttgttgtattgattagtccatttatttcagGTTTAATAGCTGATATAGACATCGAGTCAGAGAAGTTCAGATGGATGGGAAGTGCTCGTATTGACTTTTAT
upper sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0181g00250.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------------------------------------------------------------gtatgccacaagctt----ggaattagttg---atcgaatctgaatgatactttcttggctctcatctcaccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
|||||| | | || |||| || | | | || || |||| ||| | ||||| | | || | | | ||| || || || ||||| ||||||| ||||| || ||||||||||| || || ||||||||||||||||| || || ||||||||
gtatgaccaaaatttccaccacttgtttatgccatactcttggaactgcaagtgactgttgaactggatttttaagacaagctttctaagaatatgcctctggatttactagaataagctttctagtggatttgtttgat--tttgatagctct-actttgccttactgacagaattttagta--ttccagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAATATAGGTGGATGGGAAGTGCTCGTTTAGATTTCTACMapped 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|29665463|gb|CB661738.1|CB661738EST: CATTGTGCAGGGAAGGAAGAAATTTTTCAGTGTCTTGAATATGACTTGGG GTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAA
genomic: CATTGTGCAGGGAAGGAAGAAATTTTTCAGTGTCTTGAATATGACTTGGGgtatgccaca ... tacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatactttcttggctctcatctcaccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
atctcac putative branch site (score: 3)
ataataataatacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccacaagcttggaattagttgatcgaatctgaatgatactttcttggctctcatctcaccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA