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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACTAAGGCAGGAGGTAATTGTGGAGCTTGTTGATCAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaatctaatatttggtgaatatagtttttacttctaagatatggatgaagttgactgactgaacttccttgacaaccctggattatgggcatgt...

Basic information

species Oryza sativa
transcript LOC_Os01g12880.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G062953_T01 (Zea mays), 5'ss of exon 7
GGACTAAGGCAGGAGGTAATTGTGGAGCTTGTTGATCAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaa-----tctaatatttggt-gaatat---agtttttacttctaagatatgg---atgaagttgactgactgaacttccttgacaaccctggattatgggcatgt
|| ||||||||||||||||||||||| ||||| ||||| || |||||||||||||||||||| || |  ||||||||| ||||| |||||||        ||| | |||   | |||||    |  |  |  |  |  |||||     |||    ||| ||  ||  ||||    |  | | | ||            
GGGCTAAGGCAGGAGGTAATTGTGGAACTTGTGGATCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgctctttttctgaaattcatttgaatacttgaagtcctcttagtgtgatatatcttatggtagtgaatggatgtgcttctaaaatcagcataga------------

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G153138_T02 (Zea mays), 5'ss of exon 7
GGACTAAGGCAGGAGGTAATTGTGGAGCTTGTTGATCAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaatctaatatttggtgaatatagtttttacttctaag---atatggatgaagt-tgactgactgaacttccttgacaaccctggattatgggcatgt-
||| |||||||||||||||||||||| || || || || || |||||||||||||||||||| || |  ||||||||| ||||| |||||||     | || |     |||  |  |||| ||   | |    || |   ||   | |  || |  | | |   | ||    | || | |  |   |  | 
GGATTAAGGCAGGAGGTAATTGTGGAACTCGTGGACCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgtgctttatct-----gaacttcattttaacacttgaagtcatcttagtgctatatatcttatggtagtgaatggatgtgcttgaaattggcatagatg

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA14G21360.1 (Glycine max), 5'ss of exon 1
GGACTAAGGCAGGAGGTAATTGTGGAGCTTGTTGATCAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagt-----aaatctaatatttggtg-aatatagtttttacttctaagatatggatgaagttgactgactgaacttccttgacaaccctggattatgggcatgt------------------------------------------------------
||  | || |||||||| ||||| ||  | || || |||||||| ||||||||||||||||||||||  || || ||  | ||   || ||      ||  |   |   || |  |||||| |  | ||| |  | | ||   |  |  ||  ||  | |  ||| |||   |   |  || |   | ||                                                        
GGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTACACCTTGTCAACTCAACTTTgtaaggcctggaatccctttccatgatataatataatgatgactgcgtaca-atatttttaactgcttggttcatgttcattg--tatttttaataaaatgtattctttttatccaaacaatataacagttattattatggtcttttctgtctattctag

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA17G26440.2 (Glycine max), 5'ss of exon 7
GGACTAAGGCAGGAGGTAATTGTGGAGCTTGTTGATCAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagt-----aaatctaatatttggtga-atatagtttttact---tctaagatatggatgaa-gttgactgactgaacttccttgacaaccctggattatgggcatgt------------------------------------------------
||  | || |||||||| ||||| ||  | || || |||||||| |||||||||||||||||||| |  || || ||  | ||  ||| ||      ||  |   |   || |   ||||| |  | |||   |  || || |   | |  |||   ||       |   || |  |   || |||||    ||                                                  
GGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTTCACCTTGTCAACTCAACTTCgtaaggcctggaatccctttccatgatattatataatgatgactgagtacaatattttactcattgtttcgtgttcattgtatttttagtaaaatgtattatttttatccaaacaatatagtagttattattatggtcttttccgtcaatttttccag

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|218493908|gb|FG949303.1|FG949303
EST:     CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGC                         GGCATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAAC
genomic: CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaat ... ccatttacagGG-ATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAAC
EST: gi|29674265|gb|CB670540.1|CB670540
EST:     CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGC                         GGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGAC
genomic: CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaat ... ccatttacagGGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGAC
EST: gi|88395912|gb|CI593114.1|CI593114
EST:     CAGTGTCGCACTTACCAGCAGAGAGTGGTACTACTAGTTAATGCTACCGC                         GGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACCTTGCAAC
genomic: CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaat ... ccatttacagGGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGAC-TTGCAAC
EST: gi|29666463|gb|CB662738.1|CB662738
EST:     CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGC                         GGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACG
genomic: CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaat ... ccatttacagGGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACG
EST: gi|58677859|gb|CK066546.1|CK066546
EST:     CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGC                         GGATGAGGAACGGATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACG
genomic: CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaat ... ccatttacagGGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACG
EST: gi|58608171|gb|CK036204.1|CK036204
EST:     CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGC                         GGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACG
genomic: CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaat ... ccatttacagGGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACG
EST: gi|58692666|gb|CK081353.1|CK081353
EST:     CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGC                         GGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACG
genomic: CAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaat ... ccatttacagGGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACG

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: 71 (upstream exon), 75 (downstream exon)
Score: 58

GGACTAAGGCAGGAGGTAATTGTGGAGCTTGTTGATCAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGCgtgagtaaat ... ccatttacagGGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACGTGTTCTCGCAAAACACGATGCAATTGCTGCAGGCATTGCAGTTCGAGTG




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