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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgttctctttcagtttattagcccgttatacatatatgcattgtgagaagcataactatgcatgacaatcttggcttttcttttggtagttctctggtctcaaccaaactctatggttatgctgctattgttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTGGCGAAACTGCCTGTTGATGTTTTGATTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G013283_T01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013283_T01 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os04g35260.1 (Oryza sativa), 3'ss of exon 23
gttgtgttct-ctttcagtttattagcccgttatacatatatgcattgtgagaagcataactatgcatgacaatcttggcttttcttttggtagttctctggtctcaaccaaactctatggttatgctgctattgttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTGGCGAAACTGCCTGTTGATGTTTTGATTGGAAAG
||| | |||| | ||  ||    ||   | |||| ||| | |||||  | || |||| ||         ||| | ||||| | || ||| ||||||||        ||||||||| |||   | |    ||  |||  | | ||||||||||| |||||||||||||| || || ||||||||||| |||||| |||| ||| |||| |||||||||||||||||||||
gttctattctgccttttgtcatataaatctttattcatgtgtgcat-attagtagcagaa---------acatttttggcatatccttttgtagttctt-------aaccaaactttata-ctgt----ctggtgtcatgtgtagGTTGGAGCATTTGAAGGACATGAGGAATTATCACCTCTTGGCTATCATTTGGCCAAATTGCCAGTTGATGTTTTGATTGGAAAG

upper sequence: GRMZM2G013283_T01 (Zea mays), 3'ss of exon 23
lower sequence: AT1G58060.1 (Arabidopsis thaliana), 3'ss of exon 24
gttgtgttctctttcagtttattagcccgttatacatatatgcattgtgagaagcataactatgcatgacaatcttggcttttcttttggtagttctctggtctcaaccaaactctatggttatgctgctattgttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTGGCGAAACTGCCTGTTGATGTTTTGATTGGAAAG
                                      |    ||||   |||    ||||| | | || | | |||    | | ||||  |||| | | |||    |  | || | | ||   |       ||| || | |||||||| ||| |||||||  ||||||||||| |||| |||||| ||||| | || ||||| ||||||||||| || |||||||||
----------------------------------ttagttccgattgatggaatatcaactaagta-gagagttttg--catacctttgagagtttttttgtc----ctgagctttctcgt---gtgaaccctgtcttctttagGTTGGTGCTGTTGAAGGGGATGAAGAGTTGACACCACTTGGGCATCATTTAGCCAAACTTCCTGTTGATGTGTTAATTGGAAAG

upper sequence: GRMZM2G013283_T01 (Zea mays), 3'ss of exon 23
lower sequence: Vv12s0035g00800.t01 (Vitis vinifera), 3'ss of exon 22
gttgtgttctctttcagtttattagcccgttatacatatatgcattgtgagaagcataactatgcatgacaatcttggcttttcttttggtagttctctggtctcaaccaaactctatggttatgctgctattgttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTGGCGAAACTGCCTGTTGATGTTTTGATTGGAAAG
                               || |  | ||  | | |    |  | || |||   | |  |    |    || |||  | | || ||     ||| ||||  |      ||   || | |||        |||||||| ||| |||||||  ||||||||||| | ||||||||| ||||| |||| ||||| ||||||||||| || |||||||||
------------------------------aattctgacatttactttacccaataaaattattagtaattactcag----ttttttgagcatttatcaaaattcatccaa--tactcaattggactaccatt--------tagGTTGGTGCTATTGAAGGGGATGAAGAGTTGACGCCTCTTGGGCATCATTTGGCTAAACTTCCTGTTGATGTGTTAATTGGAAAG

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|12046201|gb|BF728340.1|BF728340
EST:     AGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAG                         GTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTG
genomic: AGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAGgttgtgttct ... ttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTG
EST: gi|78180848|gb|DV551221.1|DV551221
EST:     AGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAG                         GTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTG
genomic: AGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAGgttgtgttct ... ttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTG
EST: gi|6827611|gb|AW331254.1|AW331254
EST:     AGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAG                         GTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTG
genomic: AGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAGgttgtgttct ... ttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTG
EST: gi|32915243|gb|CF020055.1|CF020055
EST:     AGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAG                         GTTGGAGCTTTTGAAGGACATGGAGAGTTGTCACCTCTTGGGTATCATCTG
genomic: AGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAGgttgtgttct ... ttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTG

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: 46 (upstream exon), 46 (downstream exon)
Score: 120

GCAGTAGAGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAGgttgtgttct ... ttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTGGCGAAACTGCCTGTTGATGTTTTGATTGGAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 89

GCAGTAGAGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAGgttgtgttct ... ttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTGGCGAAACTGCCTGTTGATGTTTTGATTGGAAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 110

GCAGTAGAGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAGgttgtgttct ... ttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTGGCGAAACTGCCTGTTGATGTTTTGATTGGAAAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 68

GCAGTAGAGCCCCCTAATGAAGAAGCTATTTCCTCTGCAGTTGACTTGTTATACAAGgttgtgttct ... ttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTGGCGAAACTGCCTGTTGATGTTTTGATTGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagttctctggtctcaaccaaactctatggttatgctgctattgttttatctagGTTGGAGCTTTTGAAGGACATGAAGAGTTGTCACCTCTTGGGTATCATCTGGCGAAACTGCCTGTTGATGTTTTGATTGGAAAG
                                             ttttatct  CT-rich tract
                                        tattgttttatcta  TA-rich tract