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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g68010.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G068392_T01 (Zea mays), 3'ss of exon 4
----gttctagtacgcgcaccctatgtttgtattt-ttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
| || | | | || | || | | || || | | || ||| ||| | ||| | || | || || | |||| | ||||| ||||||||||| ||||| |||||||| ||||| |||||||| |||||||||||||| || ||||| || ||||| |||||||||||||||||||||
acttatgctgttgggttcgttgcatctatgaactgatttgccctcctctattgctct---tttattggtaactgatgctg--tctggaatttttcttcctaacagTACTCAGAGATTATGGAGCAGATTGACCGCGATGTAAAGCGCACCCACCCTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG

upper sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 4
gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctg----atgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
|| | || | | | | | | || | ||| |||| || | || | || | | | || ||| | | | | | || || || ||||||| || || ||||||||||| ||||| ||||||||||| ||||| ||||| ||||||| ||| || || |||||||| || ||||||
--tccattat-tgtatcacaattatataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaaatttc-cgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG

upper sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 4
---gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
|| | ||| | ||| | | | | | | | | | |||| || | || | | | || | | | | | | | || || || ||||||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| ||||||| ||| || || |||||||| || ||||||
ttcattattgtatcacaattatataaatctcatgctaat-gccctataatactctg-tgcaaaggctgttgtgaagcaaatctc-cttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG

upper sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
---gttctagtacgc----gcaccctatgtttgtatttttcaccagcttgca-tcattc-tgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
|| || || | || || || ||||| | ||| | || |||| | | |||||| || || |||| | | || | ||||||| || |||||||||||||| ||||| ||||||||||| || |||||| | || |||| ||| ||| | | | |||||| | ||||||
cccatttctttatgctattggactataaattggtattaggagatgatatatggtcactgatggtgttttgaattatttattacaatttgaacattttt---------agGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG

upper sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ15182 (Selaginella moellendorffii), 3'ss of exon 4
gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
| ||| | ||| || | | | ||| | || || || |||| | | || || ||||||| ||||| |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || | || |||
--------------------------------------gtttgtttacttcctttgcaatt-ccaatccaaatgga---------atttccacttcgcagGACACGGAACTTTTCGAGCAGATTGATCGTGATGTTAAGCGAACTCATCCTGATATGCAGTTTTTCTGTGGTGATAACGAGCGCGCGCACGAAAACCAG

upper sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ09811 (Selaginella moellendorffii), 3'ss of exon 4
gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
| ||| | ||| || | | | ||| | || || || |||| | | || || ||||||| ||||| |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || | || |||
--------------------------------------gtttgtttacttcctttgc-atttccaatccaaataga---------atttccacttcgcagGACACGGAACTTTTCGAGCAGATTGATCGTGATGTTAAGCGAACTCATCCTGATATGCAGTTTTTCTGTGGTGATAACGAGCGCGCGCACGAAAACCAG

Mapped 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|38565749|gb|CK085202.1|CK085202
EST:     AGCACCCATTGAGCCTTGGGAAGACAACTGCATGGAATCAGTTCTTTGAG                         TATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT
genomic: AGCACCCATTGAGCCTTGGGAAGACAACTGCATGGAATCAGTTCTTTGAGgtgcccactg ... tttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT
EST: gi|87021285|gb|CI295344.1|CI295344
EST:     GAATCAGTTCTTTGAG                         TATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT
genomic: GAATCAGTTCTTTGAGgtgcccactg ... tttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT
EST: gi|58604226|gb|CK014754.1|CK014754
EST:     AGCACCCATTGAGCCTTGGGAAGACAACTGCATGGAATCAGTTCTTTGAG                         TATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT
genomic: AGCACCCATTGAGCCTTGGGAAGACAACTGCATGGAATCAGTTCTTTGAGgtgcccactg ... tttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT
EST: gi|58652950|gb|CK041630.1|CK041630
EST:     AGCACCCATTGAGCCTTGGGAAGACAACTGCATGGAATCAGTTCTTTGAG                         TATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT
genomic: AGCACCCATTGAGCCTTGGGAAGACAACTGCATGGAATCAGTTCTTTGAGgtgcccactg ... tttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
                                         tatctttc  CT-rich tract
 ttactactaatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - -cgcaccc
- - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - -ttcacca
- - - - - - - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgttact