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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatgattcggtccttctttttgaaatccaaccttcggtgcttgcaaaattgattatgctagtttctgatagatcaattgattggactttcggtta...

Basic information

species Zea mays
transcript GRMZM5G846811_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatgattc--ggtccttctttttgaaatccaaccttcggtgcttgcaaaattgattatgctagtttctgatagatcaattg--attggactttcggtta
||||||||||| |||||||||||||||||||||||||| || || || || || |||||||||||||||||   | |  ||  ||  |||  |||||| || |||  || | ||  | |       |  |  |||  ||| ||   | ||  || ||| |||      
TGGATACCTGAGCTGAAGCATTATGCACCTGGTGTGCCTATCATCCTTGTGGGAACAAAGCTTGgtaagaaccgtgcaaggctctattttgagaaatctaatcttttgtacctgtcacaagttcggttttgattttggatggaagtagtggcatgggattttta----

upper sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G08380.1 (Glycine max), 5'ss of exon 5
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaag---aatgattcggtccttctttttgaaatccaaccttcggtgcttgcaaaattgattatgctagtttctgatagatcaattgattggactttcggtta
||||| || ||  |||||||||||||||||||||| || |||||||| || || |||||||||||||||   | || | |      |  |  ||| ||  |       |   |    | ||   |    || | || |  |   | |||| | |  | | | | || 
TGGATTCCAGAGTTGAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttattgctgcataatgtgatactgatattgagtaccatgcattcattagatgcttccctctggcttgt--ttatttaatttagtcaa-tgtggcttg

upper sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G05160.1 (Glycine max), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatgattcggtccttctttttgaaatccaaccttcggtgcttgcaaaattgattatgctagtttctgatagatcaattgattggactttcggtta
||||| || ||  |||| ||||||||||||| ||| || |||||| | || |||||||||||||||||      |||   |    ||||| |  |   |  ||  |    ||   | ||| | ||      || |   | || |||| ||   |||     | |
TGGATTCCAGAGTTGAAACATTATGCACCTGATGTTCCCATTATTTTGGTTGGGACAAAGCTTGgtaaatcaatttctacctaattttttaatgtttgatattatgatactgtgcatttgttaattgcttcttttagcacattaatttataatactactattaa

upper sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 5
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaag---aatgattcggtccttctttttgaaatccaaccttcggtgcttgcaaaattgattatgctagtttctgatagatcaattgattggactttcggtta
||||| || ||  ||||||||||||| |||||||| || |||||||| || || |||||||||||||||   | || | |      |  |  ||| ||  |       |   |    | ||      | || | || |  |   | |||| |||  | | | | || 
TGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttattgctgcataatgtgatactgatattgagtaccatgcattcattagatactgccttctggcttgt--ttatttaatttattc-attgtggcttg

upper sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G11510.1 (Glycine max), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatgattcggtccttctttttgaaatccaaccttcggtgct--tgcaaaattgattatgctagt-----ttctgatagatcaattgattggactttcggtta
||||| |||||  ||| ||||||||| |||||||| ||||||||||| || || ||||| |||||| ||| |   | | ||||||| |    ||       | |  |  |  ||   |||| |  ||  |||      |||| |||  |   |||  |   || || ||  
TGGATTCCTGAGTTGAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagatt--cttgttccttctct----aactttgtttacactaataatgtgtaattcagcataatagagaacattcttatacttatgttgtgtat-ctctcagtgt

upper sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G03660.1 (Glycine max), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatgattcggtccttctttttgaaatccaaccttcggtgcttgcaaaat-tgattatgctagtttctgatagatcaattgattggactttcggtta-
||||| |||||  ||| ||||||||| |||||||| ||||||||||| || || ||||| |||||| ||| |   | | |||||| ||      ||  || ||   | |   |  ||| || |  |  |  | | | || | |  |  |   ||    |   ||  
TGGATTCCTGAGTTGAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagatt--cttgttccttcattaccttctctgactttgtatacactcttaatgtgctccttatgttgtgtcattgttttaaagtgggggaagttacttgc

upper sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 5'ss of exon 4
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatgattcggtccttctttttgaaatccaaccttcggtgcttgcaaaattgattatgctagtttctg--atagatcaattgattggactttcggtta
||||| |||||||||| |||||||||||||||||| ||||| ||||| || || || ||||||||||||| |   ||  || |    ||   ||||  |  || | || ||||     | ||| |  ||   || |   |   |   |  |||| |  |||  | |
TGGATTCCTGAACTGAGGCATTATGCACCTGGTGTTCCAATAATTCTTGTTGGAACCAAGCTTGgtaagattatctctatcatatgcttgttaatcataattttg-tg-ttgctgttgttattttcttatcatcagctgtgagtttgtaaattgaaagttctctga

upper sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 5'ss of exon 5
TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatgattcggtccttctttttgaaatccaaccttcggtgcttgcaaaattgattatgctagtttctgatagatcaattgattggactttcggtta
||||| |||||  ||| |||||||||||| ||||| ||||| ||||| || ||||||||||||||| ||| |       |||   ||||| || | | |       |  ||    ||||       | |||     | | ||  | || ||  | |||   |  
TGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTGgttagattctcctaatccaatttttttaagtgctattaatttttttttttcaattaccagaacaagtgagctacaaatgtaatgtttataatttttctct

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|101394632|gb|EB819252.1|EB819252
EST:     GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
EST: gi|32911002|gb|CF015814.1|CF015814
EST:     GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGACGACAAGCGGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
EST: gi|116814412|gb|EC856959.1|EC856959
EST:     GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
EST: gi|22545282|gb|BU097655.1|BU097655
EST:     GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGACGACAAGCAGTTCTTTGTGGACCA
genomic: GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCA
EST: gi|32943777|gb|CF048596.1|CF048596
EST:     GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
EST: gi|211082353|gb|FK946329.1|FK946329
EST:     GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA
EST: gi|21331007|gb|BQ486388.1|BQ486388
EST:     GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG                         ATCTTCGAGACGACAAGCAGCTCTTTGTGGACCATCCTGGCGCTGACCCTA
genomic: GAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTA

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 327

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTATCACTACTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTATCACTACTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTATCACTACTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 572

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTGgtaagaatga ... tcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTATCACTACTGCTCAG