Sequence
atgc intronic sequence ATGC exonic sequencegttaggattttgctctgggatatttcataatagaattgaaacatcttgtttccaattcagagttctttatttcttttttatatattagtttcgatcaaaagttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g30460.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 7
gttaggattttgct--ctgggatatttcataatagaattg---aaacatcttgtttccaattcagagttctttatttcttttttata-----tattagtttcgatcaaa---------agttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
||| | ||||||| ||| || ||| ||| ||| ||| ||| | |||||| | || ||| |||| |||| | || | |||||| || | | | | | ||||||| ||||||||| |||||||||||||| ||||||||||||||||| ||||| || ||||||||||| ||||||||||||||
gttgtgcttttgctagctgttatttttttaaattcaataagaaaaatatcctatttccagcttagggtttcccattttttttgtttaatgtgttttagttctgagaacactatcgttgaactttatgttgtt-gcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG
upper sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 6
----gttaggattttgctctgggatatttcataatagaattgaaacatct-----------tgtttccaattcagagttctttatttcttttttatatattagtttcga--tcaaaagttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
||||| || | | ||| || || || | | || | | || || || || ||| | | | | ||| || | |||||| | | |||| | | ||||||||||| || ||||| | ||||| || ||||||||||||||||| || || ||||| || |||||||||||
gtcagttagtatatagttcttatattttgatggttatggatcatacttttgtttgtgctgatgctttcattttggagattgacttctttgaattaattaatcttttcgacattggtacttattaat--ctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
upper sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 2
----gttaggattttgctctggg--atatttcataatagaattgaaacatct--tgtttccaattcagagttctttatttcttttttatatattagtttcgatcaaaagttatctgttgtttg-cagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
||||| || | |||||| ||| ||| ||| || | || || || || ||| | | | | ||| || | ||| || || || | | | | ||||||||||| || ||||| | ||||| || ||||||||||||||||| || || ||||| || |||||||||||
gtcagttagtatatagctctgtttcatacttctgtttagttctgtttgtgttgatgctttcattttggagattgacttctttgaattaattaatcattttga-catgggtactgattaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
upper sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 6
gttaggattttgctctgggatatttcataa------tagaattgaaacatcttgtttccaattcagagt-tctttatttcttttttat----atattagtttcgatcaaaagttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
||||| |||| || | | | | ||| || || | | || || || | || | | | | || | || || |||| ||| | || || | | ||||| ||||| |||||| | | ||||||||||| || ||||||||||| ||||| |||||||| |||||||||||
gttagtgttttaacctaaggt-tctaatagagattctacttttcatatatatttttaatattttaaaatgtgagcatgagtcgttaatgggcatatattttttgtctgaacatttaatttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
upper sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
gttaggattttgctctgggatatttcataatagaattgaaacatcttgtttccaattcagagttctttatttcttttttatatattagtttcgatcaaaagttatctgttgtttg--cagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
|| | | || | || | ||||| ||| | || || || || | | ||||| | | | | | | || || || | ||||| ||||| |||||||| || ||||||| || ||||||||||| || || || ||||| ||||||||||||||
-------gttagtttctggtgacccgatgagtaaattgg--cattgtaatttcaccacaagaa-----atctgatgtttatgcacttgcctgtgttgattcttctcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
upper sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------gttaggattttgctctgggatatttcataatagaattgaaacatcttgtttccaattcagagttctttatttctttt--ttatatattagtttcgatcaaaagttatctgttgt----ttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
|| || ||| || | ||| ||| || || || | | | ||| | || | || | || | || |||| | | || || | | | ||||| || ||||| || | || || ||||| || ||||||||||| ||||||||||| || |||||||||||
gtcagttatattcaaaaagttgatatgatgtgagagtttaaagcttcttaagttc-caatttgatataattataaataatgacaataagaaattttcacttgatgagaccatttgttgatttcatctatgaatttggtgatttaatctaacagATTGAGCCAGGTGACGTTCTATGCGAAATAGAGACAGACAAAGCTACCCTTGAGTTTGAAAGTCTTGAAGAGGG
upper sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
----gttaggattttgctctgggatatttcataatagaattgaaacatcttgtttccaattcagagt-tctttatttcttttttatatatta---gtttcgatcaaaagttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
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gtttgttatg-cttaattaaaggttattgaatttcaa----gtaatattttttttcctgtttggaaaatacttgtttatctattcagcctttcctgttctcttgatcatttacttgat-ctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGGMapped 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|33674807|gb|CF303046.1|CF303046EST: AATCAAGGTAACATTGCAAAATGGAGAAAACAAGAAGGTGAAAAG ATAGAAGTTGGTGATGTGATCTGTG
genomic: AATCAAGGTAACATTGCAAAATGGAGAAAACAAGAAGGTGAAAAGgttaggattt ... ttgtttgcagATAGAAGTTGGTGATGTGATCTGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttatttcttttttatatattagtttcgatcaaaagttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
atttcttttttatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggattttgctctgggatatttcataatagaattgaaacatcttgtttccaattcagagttctttatttcttttttatatattagtttcgatcaaaagttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG