Sequence
atgc intronic sequence ATGC exonic sequenceCTTTATGCTCCTATTAGCAGTCTTTTGTACAAATTCGATCAATATACATGCTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGTTATTATATCTGCTGCGgtatgaacaaaatatctgtcgatgagaattttgtaacccaaattctatttgtctactgatgttgtataacattttttag
Basic information
species | Oryza sativa |
transcript | LOC_Os07g46640.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G137707_T02 (Zea mays), 5'ss of exon 5
CTTTATGCTCCTATTAGCAGTCTTTTGTACAAATTCGATCAATATACATGCTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGTTATTATATCTGCTGCGgtatgaacaaaatatctgtcg---atgagaattttgtaacccaaattctatttgtctactgatgttgtataac----attttttag--
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ATTCATGCTCTTGTTAGCAGTCTTTTGTACAAACTCGATAAATATACATGCTGGTCTAAATGGACTTGAAGTTGGGCAGACTATTGTTATATCTGCTGCGgtataaacaaaatatattccttatgtgacatacatgaattttgcataccactcatgtcttgttggcgtgtggttgtggttttttccag
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G827205_T02 (Zea mays), 5'ss of exon 5
CTTTATGCTCCTATTAGCAGTCTTTTGTACAAATTCGATCAATATACATGCTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGTTATTATATCTGCTGCGgtatgaacaaa--------atatctgtcg-atgagaattttgtaa---cccaaattctatttgtctactgatgttgtataacattttttag-
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ATTCATGCTCTTGTTAGCAGTCTTTTGTACAAACTCGATAAATATACATGCTGGCCTAAATGGACTTGAAGTTGGGCAGACAGTTGTTATATCTGCGGCGgtattaacagatttacagaatatattccttatgtgatgtacatgaatttttgcataccactcatgtcctgatggtgtgtggtctttttccag
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G16320.1 (Glycine max), 5'ss of exon 5
CTTTATGCTCCTATTAGCAGTCTTTTGTACAAATTCGATCAATATACATGCTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGTTATTATATCTGCTGCGgtatgaacaaaatatctgtcgatgagaattttgtaacccaaattctatttgtctactgatgttgtataacattttttag------
| |||| || || || || ||||| |||||||| ||||||||||||||||| | ||||| |||||||||||||||||||| |||| | | || ||| | | ||| | | | | || | | ||| | |||| | || |||| |||| | | | |
ATATATGGGGCTCTTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACAGTGGTTATTGCATCAGCTgtaagtatcaaa-----gcttgtaaaagtt-----aacagaatccactttggtcatggaagttg-ataataatgtggatgtgcag
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G34640.1 (Glycine max), 5'ss of exon 5
CTTTATGCTCCTATTAGCAGTCTTTTGTACAAATTCGATCAATATACATGCTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGTTATTATATCTGCTGCGgtatgaacaaaatatctgtcgatgagaattttgtaacccaaattctatttgtctactgatgttgtataacattttttag------
| |||| ||||| || || ||||| |||||||| ||||||||||||||||| | ||||| ||||||||||||||||| || |||| | | || ||| | | ||| ||| | ||||| | | | | | |||| | || ||| |||| | | | |
ATATATGGGGCTATTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACTGTGGTTATCGCATCAGCTgtaagtatcaaa-gcttgt-----aaaattt----aactgagtccactttggtcaaggaaattg-ataatactgtggatgtgcag
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0007g05920.t01 (Vitis vinifera), 5'ss of exon 5
CTTTATGCTCCTATTAGCAGTCTTTTGTACAAATTCGATCAATATACATGCTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGTTATTATATCTGCTGCGgtatgaacaaaatatctgtcgatgagaattttgtaacccaaattctatttgtctactgatgttgtataacattttttag
| |||| || || || || ||||| || || || ||||||||||||||||| | ||||| ||||||||||||||||| ||| |||| | |||| ||| ||| ||| | | | | ||| || |||| | || |||||| ||| || ||| ||
ATATATGGGACTTTTGGCTGTATTTTGCACGAACTCCATCAATATACATGCTGGTTTAAATGGCCTTGAAGTTGGGCAGACTGTTGTTATTGCATCTGCTgtaagaataaagcctt-----gtagaactgttggaatttgaattggttatggaatctgatgcatcatagcaatttacagMapped 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|38473384|gb|CF957516.1|CF957516EST: CTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGTTATTATATCTGCTGCG GTTTTGATACATAATGTAATGCGCATAGGATCTTCTACGGACATTGAAGCG
genomic: CTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGTTATTATATCTGCTGCGgtatgaacaa ... cattttttagGTTTTGATACATAATGTAATGCGCATAGGATCTTCTACGGACATTGAAGCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTTATGCTCCTATTAGCAGTCTTTTGTACAAATTCGATCAATATACATGCTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGTTATTATATCTGCTGCGgtatgaacaaaatatctgtcgatgagaattttgtaacccaaattctatttgtctactgatgttgtataacattttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC