Sequence
atgc intronic sequence ATGC exonic sequencegtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g03260.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 4
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatc---aaacctgttttcatgttcattttgaagaaattttttaa--ataaactgcaatttgtgtt-gtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
||||||| | | ||| | | ||| | | |||||| |||| | | || || ||| || | |||| | | || | ||| || | || | || |||||||||| |||||||||||||||||||| |||||| |||| |||||||| || || || ||| |||||||||||
gtatgcccactcctttgcttctcggtttatttagttgatatcttggcttctctgcctcctagtaccaaaatttaggttccctgtattttcccccttccacaatagtttgaatttcatatttgtttgcagGCTAATCCAGACTACAAGGGTGTCTGCCACATTGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatc---aaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
|| |||| | || | |||| | |||| | ||||| ||| || || |||| ||| || | | | || || |||| | | | | | |||| |||||||||||| |||||||||||||| ||||| |||||||| || |||||||| || || || ||
-----ggtatgcattctt-ttgtttttttttcaatct-tgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaac-------attgactgtgagat-tataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 4
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcat-gttcattttgaagaaatttt-ttaaataaactgcaatttgtgttgt---ttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
||| || || ||| | || || ||| || || | | ||||||| || ||| || ||| | || | |||||||| |||||||| || || |||||||| ||||||||||| || || || |||||||||||||| || |||
----------------------------taaacattagcagtttattttcatgtcattgaagtaactttaatcattaaccatcaagaaataaagttttatagaccgcataataatttatacattgcagGCTAATCCAGATTATAAAGGTGTTTGTCACGTTGCTCTAGCACAGGAAGGTCATTGCAGACCTGGAGAG
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatc---aaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
| ||| || |||| | |||| | ||||| |||| || || || | ||| || | | | || || |||| | | | | | |||| |||||||||||| |||||||||||||| |||||||||||||| || |||||||| || ||||| |||
--------gtatgcattcttttgatttttttcaatct-tgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaac-------attgactgtgagat-tataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
| || | | |||| || | ||||||| | | |||| || ||| ||| | | ||| | | || |||| ||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| ||||| |||
----------------------------------------gtatgat-ggtttgaattgattctgttttgct-tgcattcggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 4
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaa--tttg--tgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
||||| | || || | | | | | || | | | | | | | || ||| |||| | || ||| | | || | || || |||| | ||| |||||| || ||||| || || ||||| ||||| ||||||||||| ||||| ||||||||||| || || |||
gtatgatg--cctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaaggttatcatctgtcctt-------gtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 4
gtatgccgatcca--ttttcattatcttttctccaattgatagcttgt-ttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
||||||| || |||||| | | | ||||| | | | ||| | | | | | | ||| |||| ||| ||| |||||| | | || | ||||||| ||||| || ||||| ||||| ||||| ||||| ||||| ||||| ||||||||||| || || |||
gtatgcctctctggtctttcatgttttagtttccaaccactgaactatattgctgaaggtgtatcatctattcttgtttattgcactgaat--------gtaaacttta-cgtatga-gcatgcagGCCAATCCGGATTACAAAGGTGTATGCCATGTTGCCCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 3
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
| || | | ||| | | ||| | | || || | || ||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||| ||| | || ||||||
--------------------------------------------------------------gtacgtttgcggt-gtttgtatgtgattctgtcg-----ctctaacccggatttgatgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAG
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 1
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
| ||| || | | | || || | || ||||||||||||| ||||||||||||||||||||||||||||||||||| || ||||| ||||| || ||||||
--------------------------------------------------------------------gtacgtttgcggtgtttgtacgtgattcggtcgctctaacccggatttgatgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAGGAAGGTCACTGCAGTCCGGGCGAG
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 3
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
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--------------------------------------------------------------gtacgtttgcggt-gtttgtacgtgattctgtcg-----ctctaacccggatttgatgcagGCGAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAGMapped 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|29628818|gb|CB633829.1|CB633829EST: AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTGAGCAATTTCAAA GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGT
genomic: AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTGAGCAATTTCAAAgtatgccgat ... ttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
attttgaagaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG