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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCTGCCTTTGAATGTGTGGATACATTGCTGGATAGCTGTCTTGATCAAGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactgttacactaaataatttatcactttgaccgaacattccgtttaatccactgtagtaatatagatgtataggtggtgtgtaatctttaaaac...

Basic information

species Oryza sativa
transcript LOC_Os02g07120.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 26
AAAGCTGCCTTTGAATGTGTGGATACATTGCTGGATAGCTGTCTTGATCAAGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactgttacactaaataatttatcactttgaccg---aacattccgtttaatccactgtagtaatatagatgtataggtggtgtgtaatctttaaaac
|||||||||||||||||||||||||| ||  |||| || ||||||||||||||||| ||||| || || || || ||||||||||| ||||||||||||||||||||| ||| |   |  |   | ||||  |  |||       ||     |  |       |        | ||||  |     | |||| || || | | 
AAAGCTGCCTTTGAATGTGTGGATACTTTATTGGACAGTTGTCTTGATCAAGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacggtttcttcacttg--tgatcaagtcaaccatttggtatagtcctggaaaattcatgacttatcaaatgtg-ataccatctgtagtcatttagag

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA17G00570.1 (Glycine max), 5'ss of exon 26
AAAGCTGCCTTTGAATGTGTGGATACATTGCTGGATAGCTGTCTTGATCAAGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtact-gttacactaaataatttatcact-ttgaccgaacattccgtttaatccactgtagtaatatagatgtataggtggtgtgtaatctttaaaac-
|| || || ||||||||||| || ||||| |||||||| || ||||||||||||||||| |||||||| || |||||||  ||   ||||||||| | |||| || | | |||| | |   |  |  ||||||  |||    |||||  |||   ||   |  | | || || | |   |    |||   |||  ||  | | 
AAGGCGGCTTTTGAATGTGTAGACACATTACTGGATAGTTGCCTTGATCAAGTGAACCCGTCATCATTCATTGTTCCTTATCTTAAATCTGGTTTGGATGgtgagcattagttataatcttttctccatcactgctgatt--acattt-gttggttctgattcacttatctaaaaggggacccagtgcacaatacttccacct

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA07G40230.2 (Glycine max), 5'ss of exon 27
AAAGCTGCCTTTGAATGTGTGGATACATTGCTGGATAGCTGTCTTGATCAAGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtact-gttacactaaataatttatcactttgaccgaacattccgtttaatccactgtagtaatatagatgtataggtggtgtgtaatctttaaaac-
|| || || ||||||||||| || |||||||||||||| || ||||||||||||||||| |||||||| || |||||||  ||   ||||||||| | |||| || | | |||| | |   |  |  ||||||   |   | ||||  |||   ||   |  | | ||  | | |    |   |||   |||  ||  | | 
AAGGCGGCTTTTGAATGTGTAGACACATTGCTGGATAGTTGCCTTGATCAAGTGAACCCGTCATCATTCATTGTTCCTTATCTTAAATCTGGTTTGGATGgtgagcattagttataatcttttctccatcactgctaatta-cattt-gttggttctgattcacttatccaaaaggggggccagtgcacaatacttccacct

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 5'ss of exon 27
AAAGCTGCCTTTGAATGTGTGGATACATTGCTGGATAGCTGTCTTGATCAAGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagt----actgttacact---aaataatttatcactttgaccgaa--cattccgtttaatccactgtagtaatatagatgta---taggtggtgtgtaatctttaaaac-----------------------------------------------------------------------
||||| || ||||||||||| || ||| |||| || || ||||||||||||||||| || ||||| || || ||||| |  |||  ||| ||||| | ||||  ||    | | ||  | |   ||  |    |||| | |     |   || |   |||  | |||  |  |        | ||   ||| |    |  |     |||||                                                                        
AAAGCAGCTTTTGAATGTGTAGACACACTGCTAGACAGTTGTCTTGATCAAGTGAATCCTTCATCTTTCATTGTTCCCTATCTCAAATCCGGTTTGGATGgtgcgtttttatttttttatttttaacaagaccatcattcttttttacttcactttatttttttcacccttttccccccactttagtttagtttcatttcagctgctaaaagttatttcatgtttctatacttgaagtttagtttatcacttcctgaactgaaattgatttggctcttctcag

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|58654892|gb|CK043572.1|CK043572
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTAAGGTG                         ATCATTATGATGTAGAAATGCCTTGCCATCTGATTCTCTCAAAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAG
EST: gi|58672731|gb|CK061417.1|CK061417
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|2798908|gb|AA752202.1|AA752202
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|86478996|gb|CI121629.1|CI121629
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|38473429|gb|CF957561.1|CF957561
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|66914920|gb|CX101768.1|CX101768
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|163919951|gb|EG711701.1|EG711701
EST:     CGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: CGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|32948231|gb|BP184803.1|BP184803
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|58603061|gb|CK013589.1|CK013589
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCGAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|58667112|gb|CK055798.1|CK055798
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|29625622|gb|CB630633.1|CB630633
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCCTGCCCATCTGATTCTCTC
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCC-ATCTGATTCTCTC

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: 69 (upstream exon), 75 (downstream exon)
Score: 34

AAAGCTGCCTTTGAATGTGTGGATACATTGCTGGATAGCTGTCTTGATCAAGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG




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