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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAAATGAGCAAGCAAGAATGGAAGTTCTTAAAATCCATGCTGCTGGTATTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgtcttatttaacttccttatcaacttgggcaaccttcctgactctggtggttttag

Basic information

species Oryza sativa
transcript LOC_Os02g10640.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10640.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 8
ACCAAATGAGCAAGCAAGAATGGAAGTTCTTAAAATCCATGCTGCTGGTATTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtt---tgtcttattta-----acttccttatcaacttgggcaacctt-cctgactctggtggttttag
||| || |||||| |||||||||||||||| ||||||||||| || ||||| ||||||||||| || ||||||||||| ||||| || ||||| ||||| |||||||   ||| ||||| |     |    || |||   |     |   |  ||| |||||  |||||| ||
ACCCAACGAGCAATCAAGAATGGAAGTTCTAAAAATCCATGCAGCCGGTATCGCCAAGCATGGGGAGATTGATTATGAAGCAGTCGTGAAACTAGCTGAAgtgagttagttgtgttattcatatctaacctctaatcccatcctatagtttcaccttactctcctggtttcag

upper sequence: LOC_Os02g10640.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G171604_T01 (Zea mays), 5'ss of exon 8
ACCAAATGAGCAAGCAAGAATGGAAGTTCTTAAAATCCATGCTGCTGGTATTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtt--------tgtcttatttaacttccttatcaacttgggcaacctt-cctgactctggtggttttag
||| || |||||| |||||||||||||||| ||||||||||| |||||||||||||||||||| |||||||||||||| ||||| || ||||| ||||| |||||||        | || ||| |||| || | |||   |||   |   |  ||| |||||  |||||||||
ACCCAACGAGCAATCAAGAATGGAAGTTCTAAAAATCCATGCAGCTGGTATTGCCAAGCATGGGGAAATTGATTATGAAGCAGTCGTGAAACTAGCTGAAgtgagttagttgtattatcatatctaacctc-taatcccattgtatagtttcaccttactctcctggttttag

upper sequence: LOC_Os02g10640.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 8
ACCAAATGAGCAAGCAAGAATGGAAGTTCTTAAAATCCATGCTGCTGGTATTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgtcttatttaacttc---cttatcaacttgggcaaccttcctgactctggtggtt--ttag-------------------------------
 || ||||||||| |  | |  ||  || | |||||||||||  |||| ||| | ||||||||||| ||||||||||||||  |||||||||| ||||||||    |   | | ||    | |     | |    ||| | | | ||    ||    |   ||  |||                                
GCCTAATGAGCAATCTCGCACAGAGATTTTGAAAATCCATGCATCTGGCATTACTAAGCATGGAGAGATTGATTATGAGGCTATTGTTAAACTTGCTGAGgtacagtgtccctgttcttgtccgcatctcttggtttgtgtaccgttgtgaacgaatggaattgcttatctggcaacgggccatacaatgtttattgctt

upper sequence: LOC_Os02g10640.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S13_419V6.1 (Physcomitrella patens), 5'ss of exon 8
ACCAAATGAGCAAGCAAGAATGGAAGTTCTTAAAATCCATGCTGCTGGTATTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtg-agtttgtcttattt----aacttccttatcaacttgggcaaccttcctgac--tctggtggttttag-----------------------------
||||||||| ||  |  | |  ||  || | || || |||||  |||||||| | ||||||||||| |||||||| |||||  |||||||||| || |||||  ||| | |||  |||    ||| |  |  | ||  || |   | |  |      | || | |  |                                
ACCAAATGAACAGTCTCGTACAGAGATTTTGAAGATTCATGCATCTGGTATTACGAAGCATGGAGAGATTGATTACGAGGCTATTGTTAAACTTGCCGAGgtacagtatttctgctttcgtaaacattatccttaatctgcgtgccatcacaagaggtatgatagactggaactgtatttatagaagtgagttgtacggt

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|89194901|gb|CI003365.1|CI003365
EST:     ATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: ATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|163917943|gb|EG715243.1|EG715243
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|58608391|gb|CK036424.1|CK036424
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|86539950|gb|CI180156.1|CI180156
EST:     AGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: AGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|218483516|gb|FG958130.1|FG958130
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|218493541|gb|FG956814.1|FG956814
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|218480375|gb|FG953360.1|FG953360
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTG
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTG
EST: gi|396941346|gb|HO188555.1|HO188555
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|88991579|gb|CI019757.1|CI019757
EST:     AACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: AACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|25778007|gb|CA752759.1|CA752759
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|8955808|gb|BE229613.1|BE229613
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTRCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|58687304|gb|CK075991.1|CK075991
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|88987917|gb|CI017980.1|CI017980
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|86477906|gb|CI120539.1|CI120539
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|218501848|gb|FG946073.1|FG946073
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|89195758|gb|CI007177.1|CI007177
EST:     TTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|25778017|gb|CA752769.1|CA752769
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|58687840|gb|CK076527.1|CK076527
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|33795428|gb|CF323584.1|CF323584
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGNGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGC
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGG-GGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGC
EST: gi|218486211|gb|FG960168.1|FG960168
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|89195854|gb|CI007273.1|CI007273
EST:     GCATGGAGAAATTGATTATGAGGCAGTTGTTAAGCTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: GCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|163925709|gb|EG714545.1|EG714545
EST:     TTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|3759665|gb|C96923.1|C96923
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|27577669|gb|CB000364.1|CB000364
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|58587300|gb|CF985608.1|CF985608
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTACACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|55408414|gb|CV720790.1|CV720790
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|58587845|gb|CF986153.1|CF986153
EST:     TGCCAAGCATGGAGAAATTGGGGTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TGCCAAGCATGGAGAAATT-GATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|89198083|gb|CI117561.1|CI117561
EST:     CAGTTGTTAAACTGTCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: CAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|38480216|gb|CF964305.1|CF964305
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
EST: gi|38479537|gb|CF963642.1|CF963642
EST:     TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAG                         GGCTTCAATGGGGGTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT
genomic: TTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 72 (downstream exon)
Score: 64

ACCAAATGAGCAAGCAAGAATGGAAGTTCTTAAAATCCATGCTGCTGGTATTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgt ... gtggttttagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCTGCAATTCGTGCTGAACGGGACTACGTTGTCCATGAGGACTTCATGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAAATGAGCAAGCAAGAATGGAAGTTCTTAAAATCCATGCTGCTGGTATTGCCAAGCATGGAGAAATTGATTATGAGGCAGTTGTTAAACTGGCTGAGgtgagtttgtcttatttaacttccttatcaacttgggcaaccttcctgactctggtggttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA