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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaacatattctccaatctccacggtggcacggttgctctatatctcattaggcaatttaggatgcaccttgtatttgctaaaaaaggaaatattctggccttttaattcttacattatctattagtcaaaacacaaagtggtcaagaaagtttatcactattggttaataccatttcacag

Basic information

species Oryza sativa
transcript LOC_Os07g12530.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12530.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G031780_T02 (Zea mays), 5'ss of exon 6
GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca-tattctccaatctccacggtggcacggttgctctatatctcattaggcaatttaggatgcaccttgtatttgctaaaaaaggaaatattctggccttttaattcttacattatctattagtcaaaacacaaagtggtcaagaaagtttatcactattggttaataccatttcacag
|||||||||||| ||||||||||||||||||||||| ||||| ||||| ||||| ||||||||||||| ||||| || |||| ||| |||||||||||||| | || | || || | | || ||| | || || || | || || | || || || || | ||| | | |||
GTTTGGAAGCTTAATTTCATGTGAATCCTTCCATGCTGATGTACATGCTGGAAACCTATGGTTGCTCCGTGATGGGCGAATTGGTTTTATTGATTTTGgtatgctgtagtaatttc---tccctatagtttttacattggttgat----tatcagtcggtt------acattgtaaatgtgatagaacatgaatcacatcacacaactaag--------------------------------------------------------------------------

upper sequence: LOC_Os07g12530.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA14G36520.1 (Glycine max), 5'ss of exon 7
GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaacatattctccaatctccacggtgg-cacggttgctctatatctcattaggcaatt----taggatgcaccttgtatttgctaaaaaaggaaatattctggccttttaattcttacattatctattagtcaaaacacaaagtggtcaagaaagtttatcactattggttaataccatttcacag
||||||||| ||| || |||||||||| || ||||||||||| |||||||||||| | ||| | || || ||||| ||| |||| |||||||| || |||||| || ||| | | | | |||| | | | | || ||| || || | | | || | ||||||| |||
GTTTGGAAGTTTGCTTGCATGTGAATCTTTTCATGCAGATGTACATGCAGGAAATCTGTGGCTTCTACGTGATGGCCGTATTGGGTTTCTTGACTTCGgtatgcttgattatctttgtgcatatttatagatatggtt--ttaactttttgttgtgcatttgtcatatgttaatgttctaatgtttcaaaaaagtctata-----------------------------------------------------------------------------------------

upper sequence: LOC_Os07g12530.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G05200.1 (Arabidopsis thaliana), 5'ss of exon 8
GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaacatattctccaatctccacggtggcacggttgctctatatctcattaggcaatttaggatgcaccttgtatttgctaaaaaaggaaatattctggccttttaattcttacattatctattagtcaaaacacaaagtggtcaagaaagtttatcactattggttaataccatttcacag
|||||||||||| || | |||||| ||||||||| ||||| ||||||||||| |||||| || | || ||||| || |||| |||||||||||||||| | | | |||| | || ||| || || | || | | | || || || || | | ||||| | | | || | | | ||| || | | |||| || || || ||||| |||| | ||| || || |
GTTTGGAAGCTTACTTGCTTGTGAAAGCTTCCATGCTGATGTACATGCAGGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTGATTTTGgtaaatcatactctctcaagcctaattagtgcaacatttcttgcctactt---------acctctgactcatctattaat-acagaaaaatgcagtctttt--tccataaatactcttcctttttattggt-aattttttgtgtattcaagtaagtat-ccacatttttttcag------------

upper sequence: LOC_Os07g12530.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv13s0067g03210.t01 (Vitis vinifera), 5'ss of exon 8
GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaacatattctccaatctccacggtggcacggttgctctatatctcattaggcaatttaggatgcaccttgtatttgctaaaaaaggaaatattctggccttttaattcttacattatctattagtcaaaacacaaagtggtcaagaaagtttatcactattggttaataccatttcacag
|||||| || ||| || | |||||| |||| ||||||||||| |||||||| ||||| |||||||| || ||||| || |||| |||||||||||||||||| ||| |||| | | | | | | | | | | | | || | | ||| || || ||| || || || | | ||
GTTTGGTAGTTTGCTTGCCTGTGAAACCTTTCATGCAGATGTTCATGCAGGCAATTTGTGGTTGCTACGTGATGGCCGCATTGGGTTTCTTGATTTTGgtatg---cattttctttttgcactgggttaactca-tagtttggtttgttat------agctttgatcttttccatacatggccaaacagtgtatcttatatggtagta----------------------------------------------------------------------------

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|29615294|gb|CB620306.1|CB620306
EST:     AGGAAATTTATGGTTGCTCCGAGATGGACGTGTCGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
genomic: AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
EST: gi|29615506|gb|CB620518.1|CB620518
EST:     AGGAAATTTATGGTTGCTCCGAGATGGACGTGTCGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
genomic: AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
EST: gi|29615267|gb|CB620279.1|CB620279
EST:     GAGATGGACGTGTCGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
genomic: GAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
EST: gi|29677141|gb|CB673416.1|CB673416
EST:     AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
genomic: AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
EST: gi|29615076|gb|CB620089.1|CB620089
EST:     AGGAAATTTATGGTTGCTCCGAGATGGACGTGTCGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
genomic: AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
EST: gi|29619071|gb|CB624083.1|CB624083
EST:     AGGAAATTTATGGTTGCTCCGAGATGGACGTGTCGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
genomic: AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
EST: gi|29615292|gb|CB620304.1|CB620304
EST:     AGGAAATTTATGGTTGCTCCGAGATGGACGTGTCGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
genomic: AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
EST: gi|33796723|gb|CF324229.1|CF324229
EST:     AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTG-AANTGGAGGTCTTT
genomic: AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAA-TGGAGGTCTTT
EST: gi|29615297|gb|CB620309.1|CB620309
EST:     AGGAAATTTATGGTTGCTCCGAGATGGACGTGTCGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
genomic: AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
EST: gi|29615223|gb|CB620236.1|CB620236
EST:     AGGAAATTTATGGTTGCTCCGAGATGGACGTGTCGGATTTCTTGATTTTG                         GAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT
genomic: AGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaaca ... catttcacagGAATTGTTGGCCGGATATCGCCAAGGACCTGGGCTGCAATGGAGGTCTTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTGgtatgtaacatattctccaatctccacggtggcacggttgctctatatctcattaggcaatttaggatgcaccttgtatttgctaaaaaaggaaatattctggccttttaattcttacattatctattagtcaaaacacaaagtggtcaagaaagtttatcactattggttaataccatttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA