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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatccggattggcttctctccccgttttccagtgttctattgtcgattgcgcccaggggttggtctgatcagctatttaccgattgtggcgtttt...

Basic information

species Oryza sativa
transcript LOC_Os03g48930.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g48930.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G097164_T02 (Zea mays), 5'ss of exon 2
GAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatccggattggcttctctccccgttttccagtgttctattgt-cgattgcgcccaggggttggtctgatcagctatttaccgattgtggcgtttt
|||||| ||||||||||| |||||||| |||| ||||||||||   ||||||||| ||||||| ||||| |||||||| |||||||| ||||| || |||||||  ||||| |||    |   | | |  |||      ||     || | |  |  ||   || | | | | || |  |      | ||| |     |  
GAAGAACCTCCACCTGTACCAGTTCCGGAACACCATCCCGCTCTCAACCGCCGCCGCCGCCAACTTCACACGCGGCGAACTCGCCACAGCCCTTCGCAAGgtactaatccgaattaatcttgtttctctctttgtgcgatttgggcgttccaaggttccattggatggatattattaaatggcgttcaatttttttagtc-

upper sequence: LOC_Os03g48930.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G111566_T01 (Zea mays), 5'ss of exon 2
GAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatccggattggcttctctccccgttttccagtgttctattgtcgattgcgcccaggggttggtctgatca--gctatttaccgattgtggcgtttt--
|||||| ||||||||||| ||||||||||||| |||||||||    ||||||||  ||||||| ||||| ||||||||||||||||| ||||| || |||||||| ||||  ||     |   | | |  |||   | |||     |      | ||  |  ||| |  ||  | |  |    ||  || |  | | ||||   
GAAGAACCTCCACCTGTACCAGTTCCGCAACACCATCCCGCTGTCAACCGCCGCTGCCGCCAACTTCACACGCGGCGAGCTCGCCACAGCCCTTCGTAAGgtaccaatccaaatcaatcttgtttctctcttt---gcgttactgggcttgccgtgcaaaaaggtcgagcttttaaagggggattggcgctc-tagagtttggt

upper sequence: LOC_Os03g48930.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G38970.1 (Glycine max), 5'ss of exon 2
GAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatccggattggcttctctccccgttttccagtgttctattgtcgattgcgcccaggggttggtctgatcagctatttac-cgattgtggcgtttt--
||||||  ||  | ||||||||||||| |||  |||||| || | |||||||||| ||||||||||||| || ||||| |||||||| || || || |||||| |  ||   |     |   |      |  ||   | |   | | |        |  |  |    |    |  | | |||||  |  |||   |  |||  
GAAGAACGTCGCCTTGTATCAGTTCCGTAACGGCATCCCTCTTACCACCGCCGCCGCCGCCAATTTCACGCGTGGCGAACTCGCCACTGCTCTCCGCAAGgtatct-tctaaaccctatctcccatatatcatctcctttctcacttttaggaaaacaaattgagaagctaaa--atcaatttatgcatttgctccaatttag

upper sequence: LOC_Os03g48930.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G44200.1 (Glycine max), 5'ss of exon 2
GAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatccggattggcttctctccccgttttccagtgttctattgtcgattgcgcccaggggt-tggtctgatcagctatttaccgattgtggcgtttt----
||| ||  ||  | ||||||||||||| |||  |||||| |||| |||||||||| ||||||||||||| || ||||| || ||||| || || || |||||| |  | |  |    |       | | | |  || ||| || ||| |  |  |    |||         | |  |||||    |   || ||   || |    
GAAAAACGTCGCCTTGTATCAGTTCCGTAACGGCATCCCTCTCACCACCGCCGCCGCCGCCAATTTCACACGTGGCGAACTTGCCACTGCTCTCCGCAAGgtatctcttctaa---accctaactctcatatatca-tgtcct-ttggctctcacttataggaaaacaaattaagaagctaaaatcaatttatgctcttattcat

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|88204434|gb|CI204283.1|CI204283
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|88214715|gb|CI214564.1|CI214564
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|86528888|gb|CI169094.1|CI169094
EST:     CGCCACCGCCTTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|88329763|gb|CI651427.1|CI651427
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|428606|gb|D24758.1|D24758
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|88201980|gb|CI202335.1|CI202335
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|88975935|gb|CI024186.1|CI024186
EST:     CTCGCCACCGCCCTGCGGAAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTTT
genomic: CTCGCCACCGCCCTGCGG-AAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATG--TT
EST: gi|58685422|gb|CK074109.1|CK074109
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|88339390|gb|CI635368.1|CI635368
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGGTGGATA
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATA
EST: gi|55431314|gb|CV728671.1|CV728671
EST:     GCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: GCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|87007174|gb|CI277249.1|CI277249
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|87032562|gb|CI266202.1|CI266202
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|88214706|gb|CI214555.1|CI214555
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|29659834|gb|CB656109.1|CB656109
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|89195938|gb|CI007357.1|CI007357
EST:     TTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: TTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|86824114|gb|CI260755.1|CI260755
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|86422544|gb|CI060117.1|CI060117
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
EST: gi|88349785|gb|CI632920.1|CI632920
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTANTATGTNAACGTGTTGCTTGGTGGATA
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATA
EST: gi|33678293|gb|CF306532.1|CF306532
EST:     CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAG                         AATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT
genomic: CCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGT

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), 61 (downstream exon)
Score: 46

GAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatcc ... ttccttgcagAATCCGTACTATGTCAACGTGTTGCTTGCTGGATATGATTCGGATGTTGGTGCCTCTTTGTATTACATTGACTACATCGCAACATTCCATAAGATCGAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGCGAGCTCGCCACCGCCCTGCGGAAGgtaccgatccggattggcttctctccccgttttccagtgttctattgtcgattgcgcccaggggttggtctgatcagctatttaccgattgtggcgtttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccccg