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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAATCAGGTACTCTGTTTGACAACTTCCTTATTACTGACGACCCTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgttcttcacctagcttttaccgtgtaatagtttcgttatcgacccaacattctctaacattagtgaatcttgtag

Basic information

species Oryza sativa
transcript LOC_Os07g14270.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 10
GTCAAATCAGGTACTCTGTTTGACAACTTCCTTATTACTGACGACCCTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgttcttcacc-tagc-ttttaccgtgtaatagtttcgttatcgacccaacattctctaacattagtgaatcttg-tag
|| ||||| || ||||||||||||||| || | || ||||| |||||||  ||||||||||| || ||||||||||| ||||||||||||||||| || |||  ||| || |  || | | | ||   ||||    |   ||||  |  || ||| | |||||  |  |    |||   ||
GTTAAATCGGGCACTCTGTTTGACAACATCATCATCACTGATGACCCTGCCTTGGCCAAGACTTTTGCAGAGGAGACCTGGGGCAAGCACAAGGAGgtttgtttttcctctcagtaacatctcactcagtaactcatggtttattcaggca-catgcactaactatgcttgtccttaacag

upper sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 10
GTCAAATCAGGTACTCTGTTTGACAACTTCCTTATTACTGACGACCCTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgttcttcacctagcttttaccgtgtaatagtttcgttatcgaccca-acattctctaacattagtgaatcttgtag-
|| |||||||| ||| ||||||||||| || | || ||||| || |||| |||||||||||| || ||||||||||||||||||||||||||||| || |||  || | | | || |   |  |    | ||  |  |   | ||  ||  ||| | |||||  |  ||   ||| |   
GTTAAATCAGGCACTTTGTTTGACAACATCATCATCACTGATGATCCTGCGTTGGCCAAGACTTTTGCAGAGGAGACATGGGGCAAGCACAAGGAGgtgtgtttttttcctcgtaacagctctcaatcagtaactcagg-gttgattcatgcatgcactaactatgttggtccttatcag

upper sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 10
GTCAAATCAGGTACTCTGTTTGACAACTTCCTTATTACTGACGACCCTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgttct--tcacctagcttttaccgtgtaatagtttcgttatcgacccaacattctctaacattagtgaat-cttgtag
|| ||||| |||||| ||||||||||  || | |||||||| || |||||||  || |||    | |  || || |||||||||||||||||||||||| ||| ||||   |||  | |||||    ||  || |       |  ||    |   ||  |||    | ||  | |||| ||
GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAGTATGCTAAGCAGCTGGTTGAAGAAACATGGGGCAAGCACAAGGATgtaagtctttctatccactgatcttttggtatgctattg-------aaagatatgat-ctccttaatgaaaatgtgttcttgcag

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|14192066|gb|AU184277.1|AU184277
EST:     CTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGAT                         GCTGAGAAGGCTGCTTTTGACGAGGCAGAG
genomic: CTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgtt ... aatcttgtagGCTGAGAAGGCTGCTTTTGACGAGGCAGAG
EST: gi|27548814|gb|CA766773.2|CA766773
EST:     GAGACAAGGGGCAAGCACAAGGAT                         GCTGAGAAGGCTGCTTTTGACGAGGCAGAGAAAAAGAAGGAAGAGGAGGTA
genomic: GAGACATGGGGCAAGCACAAGGATgtatgtcgtt ... aatcttgtagGCTGAGAAGGCTGCTTTTGACGAGGCAGAGAAAAAGAAGGAAGAGGAGGTA
EST: gi|58679227|gb|CK067914.1|CK067914
EST:     CTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGAT                         GCTGAGAAGGCTGCTTTTGACGAGGCAGAGAAAAAGAAGGAAGAGGAGG
genomic: CTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgtt ... aatcttgtagGCTGAGAAGGCTGCTTTTGACGAGGCAGAGAAAAAGAAGGAAGAGGAGG
EST: gi|66915891|gb|CX102739.1|CX102739
EST:     CTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGAT                         GCTGAGAAGGCTGCTTTTGACGAGGCAGAGAAAAAG
genomic: CTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgtt ... aatcttgtagGCTGAGAAGGCTGCTTTTGACGAGGCAGAGAAAAAG
EST: gi|8856749|gb|AU094067.1|AU094067
EST:     CTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGAT                         GCTGAGAAGGCTGCTTTTGACGAGGCAGAG
genomic: CTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgtt ... aatcttgtagGCTGAGAAGGCTGCTTTTGACGAGGCAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAATCAGGTACTCTGTTTGACAACTTCCTTATTACTGACGACCCTGAGTTGGCCAAGACATTCGCAGAGGAGACATGGGGCAAGCACAAGGATgtatgtcgttcttcacctagcttttaccgtgtaatagtttcgttatcgacccaacattctctaacattagtgaatcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA