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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattatgtatgcctcatttctgttgtttgatggcaattatcttgaaatcctatgttcccatcgcatgcatttaatacgataaatatgttatgacttcctcactgtgtttgcagtctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA

Basic information

species Zea mays
transcript GRMZM2G118286_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 7
gtaagattatgtatgcc-tcatttc-tgttgtttgatggcaattat-cttgaaatcctatgtt----cccatcg----catgcatttaat----acgataaatatgttatg---actt-cctcactgtgtttgcag-tctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA
||||||||||| || || ||||  | ||||||| | || ||    |  || |    |||||||    | ||  |    |||  ||||||     | ||  |||    ||||   | ||   |||   ||  |  ||  |||  | | |  | |||||||||||||||||| ||||||||||||||| |||||||| ||||| || ||||||||||| |||||||| |||||||||||| ||||||| ||||| |||||||||||||||
gtaagattatgaataccatcatcccatgttgttagttgccatccttgtttaatgaactatgtttaaacacaatgaaatcataaatttaaacacaatgaagaatgaactatgcttatttgtttcaacatgcatagagacctgggaattaacaagtttatgcaatttcagGGTTCCAATAGGGCAAGGGTATGGTCTTACTGAGACATGTGCTGGAGGAACATTTTCTGAGTATGATGACCCATCTGTTGGTCGCGTTGGTGCTCCACTA

upper sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 6
gtaagattatgtatgcctcatttctgttgtttgatggcaattatcttgaaatcctatgttcccatcgcatgcatttaatacgataaatatgttatgacttcctcactgtgtttgcagtctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA
                                              |  |||  | |      ||  |||| | ||  |  | |     |   |    | |   | | | |||    | | ||||| |||     | | || |||||| ||||||||||| ||||| |||||||| || || ||||||||||| ||| |||| || || | ||| || |||||||| || ||||||||  | ||  | 
----------------------------------------------tagaattgtctagctttat--catgtactttttctgttttgctttacagatttcctgtattatcttttttctgtcacatttatatttggttttcattttcagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT

upper sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 6
gtaagattatgtatgcctcatttctgttgtttgatggcaattatcttgaaatcctatgttcccatcgcatgcatttaatacgataaatatgttatgacttcctcactgtgtttgcagtctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA
                                    | || ||| |  |        | |   |  | | |   ||  |    |     | ||  |  | | | | | |  |||| |||    ||| ||||  | |   ||  ||||| |||||||| || ||||| |||||||| || || ||||||||||| |||||||| || ||   |||||| ||||||||||| ||||||||  | || || 
-----------------------------------aggaaatatttcta--------gcttttactgta-gtgctttttcttttttgctttttgcgtttcctttattattcttgctgtc----atttataatttatggtcatattcagTGCTCCAATCGGTCAAGGATATGGTCTTACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTCGGCCGTGTTGGACCACCTCTT

upper sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 6
gtaagattatgtatgcctcatttctgttgtttgatggcaattatcttgaaatcctatgttcccatcgcatgcatttaatacgataaatatgttatgacttcctcactgtgtttgcagtctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA
                                 |  | || |||       | ||   ||    ||   ||| |||  |    | | |   ||  |  | | | | | | |    | ||||  ||| ||||  ||||||    |  || |||||||| || ||||| |||||||| || || ||||||||||| |||||||| || ||   |||||| |||||||| || ||||||||  | || || 
---------------------------------aaaggaaatat-------tactggcttttactcaagtgctttttcttttttgattt--ttgcgtttcctttattattt----attctgtgatttataa--tttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT

upper sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagattatgtatgcctcatttctgttgtttgatggcaattatcttgaaatcctatgttcccatcgcatgcatttaatacgataaatatgttatgacttcctcactgtgtttgcagtctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA
                                |    | | |  | ||||    ||| | |     || |||   |  | | ||| || | ||     | |||  |  | | |    ||| ||| |||||   ||         ||||||||||||| || || || ||||| || || || ||||||||||| || || || || |||| ||| |||||||| || || ||||||||||||||||| 
--------------------------------gtaaacgaat-ccctgaa----tatctccttgaggcttgctactc-tccaatatatctttt---cgtccctttccatttctatgatctaacactgata---ttc-------ctcagGGCTCCAATCGGTCAGGGATATGGGCTCACAGAGACTTGTGCTGGTGGAACCTTCTCGGAGTTTGAGGACACATCCGTTGGCCGTGTTGGTGCTCCACTT

upper sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 8
gtaagattatgtatgcctcatttctgttgtttgatggcaattatcttgaaatcctatgttcccatcgcatgcatttaatacgataaatatgttatgacttcctcactgtgtttgcagtctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA
                                       ||| |   ||||  ||  | |  ||    |||   |  |  |    | ||||  ||    ||||  || |  ||| | | ||   |   | |  | |   || |||||| ||||||||||  ||||| ||||| ||||| || | ||||||||| || |||||||| ||||||||||| |||||||| |||||||||||||||||||| 
---------------------------------------att-taaggaaacacttagctggca----atgtcctacaatcatgcagtatgcaatattatccttcctcttgttgtaat-tgctctaagtgaactgt---cattttcagTGCTCCAATAGTTCAAGGGTATGGCCTGACAGAGAGTTGTGCTGGTGGTACATTTTCCGAGTATGATGATACATCTGTTGGTCGTGTTGGTGCTCCACTT

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|211356217|gb|FL190937.1|FL190937
EST:     GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG                         GGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
genomic: GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
EST: gi|20802928|gb|BQ293978.1|BQ293978
EST:     GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG                         GGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
genomic: GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
EST: gi|211356219|gb|FL190939.1|FL190939
EST:     GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG                         GGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
genomic: GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
EST: gi|211130815|gb|FL468263.1|FL468263
EST:     AGATACTCAGAGATTTATCAATATATGCYTTGG                         GGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGRAGGGAC
genomic: AGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
EST: gi|211356216|gb|FL190936.1|FL190936
EST:     GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG                         GGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
genomic: GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
EST: gi|22715219|gb|BU197644.1|BU197644
EST:     GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG                         GGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
genomic: GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
EST: gi|26456576|gb|CA828159.1|CA828159
EST:     GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG                         GGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
genomic: GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
EST: gi|78026723|gb|DV495110.1|DV495110
EST:     GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG                         GGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
genomic: GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
EST: gi|211356220|gb|FL190940.1|FL190940
EST:     GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG                         GGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC
genomic: GGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGAC

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), 49 (downstream exon)
Score: 140

GAAAGGTGCGTGCTATTTTGGGAGGAAAGATTCGGTTTGTACTTTCAGGTGGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

GAAAGGTGCGTGCTATTTTGGGAGGAAAGATTCGGTTTGTACTTTCAGGTGGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 156

GAAAGGTGCGTGCTATTTTGGGAGGAAAGATTCGGTTTGTACTTTCAGGTGGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 72

GAAAGGTGCGTGCTATTTTGGGAGGAAAGATTCGGTTTGTACTTTCAGGTGGAGCACCTCTATCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtaagattat ... gcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgacttcctcactgtgtttgcagtctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA
                              attgataa  TA-rich tract