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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 7
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
|||||  ||  |  |   || |  || | | |  |||   ||  |  ||| |      |   | || |   | | |   |  |  | || | ||||  | | ||   ||||      | | || |      | ||||||||||||||||||||| ||| |||||||||| |||||| | |||||||||||||||||||| ||||| |||||||||||||||||||||||||| ||||
gtaggtctcccctggctgtgctctttttttggactgta-gccatggtcaaagtaattatgttggtttac--atcctcaagcattttttt-gcttttattctgat--aattcgttgatgctatgattgatgtttgcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 7
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
|||||  ||  |  |   || |  || | | |  |||   ||  |  ||| |      |   | || |  |  | |   |  |  | || | ||||  | | ||   ||||      | | || |      | ||||||||||||||||||||| ||| |||||||||| |||||| | |||||||||||||||||||| ||||| |||||||||||||||||||||||||| ||||
gtaggtctcccctggctgtgctctttttttggactgta-gccatggtcaaagtaattatgttggttta-cattcctcaagcattttttt-gcttttattctgat--aattcgttgatgctatgattgatgtttgcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 7
------------------gtaggcttctgccagtattgtttgttatatagtgtgtgcaccc-----agaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                  ||    ||    |   |||| |   |||  |   | || || |     |    ||| || |      | |||||||      ||   |||  ||    ||  ||  ||| | ||      | |  ||| |  ||    |||||||||||| ||||| || ||| |||| ||||| |||||| | |||||||||||||||||||| || || |||||||| ||||| ||||| || |||||||
gtatgttagcaccaccttgtcacattaattctacattgctacctatgcaaattttgtactctttctaatctaattatggtaatttgcttcagta--tacatttcttcaagttcaagttatgtccaattttatcacca-ctgacttgat--tatgctgcagAATAATCTTCATGAACTTTGGTCTCTTCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAGACTTTTGATGATTGGTTCCAAATCTCAGGGGAAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 7
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatg-gcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                                    |||      | |     ||||   |  | | | |     ||||   |  |||   |  |    |  || |  |  |        |  ||  ||   |  |||||||| || ||||| |||||| |||| ||||| ||  | || || ||||| ||||| ||||| ||||| |||||||||||||||||||| ||||| ||||
------------------------------------tgcttttctaccttgttttgaaatcttaattattttttttgtttgtttgtatgcatcctcaaat--atttactagtgtctattatcacttttattggcacagAATAACCTTCATGAACTCTGGTCTCTTCTCAACTTTCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                     |||  || |    | |    ||    || |  |||  ||     | ||| |   ||||    ||  | |||  ||  | | || || ||||       ||||     || | |||||| ||||| ||||| ||||||||||| ||||| ||  |  | |||||||||||||| ||||| ||||| |||||||||||||||||||| ||||| ||||
---------------------ttgaaatctga-atttttttccttttcatttgttgcata---ggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttct-------tttg-----acgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 7
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                      ||  || |      |    ||    || || |||  |    |  |  |||   ||||    ||  | |||  ||  | | || || ||||       ||||     | || |||||| ||||| || || ||||||||||| ||||| ||  |  | |||||||||||||| ||||| ||||| |||||||||||||||||||| ||||| ||||
----------------------tgaaatctgaatcttatttccctttcattggttgcatgtgtaagcgataa---tgttaatacacttaagtaattaatgtgatttgtttct-------tttg-----atattgcagAACAATCTTCACGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 7
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattcta-gtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                                | ||     | ||   | |  ||||   | ||   | | |   | |||| |  |||   |  |    |  || |  |  |  ||    | |  | | |     ||||||||||| ||||| |||||| |||| ||||| ||  | || || ||||| ||||| ||||| ||||| |||||||||||||||||||| ||||| ||||
--------------------------------tatgcttttctagcttatt--ttgaaatctgaacta-ttatttttttgt-ttgtatgcatcctcaaat--atttactggtgtgtattatctctttcaatggcacagAATAATCTTCATGAACTCTGGTCTCTTCTCAACTTTCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------------------------gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattct--agtccggtttgctgcta-------catg---gcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                                                   || | | || | |  ||||  ||||  |       | |    |   |  || |||    |  |  |  |  |  |   | |   | ||| | |||    ||   ||| | |  || | | | | ||  ||       |||    |||||||||||||||||| || |||||||| || |||||  | || ||||| || ||||| || || || || |||||||||||||||||||||||||| || |
gtgtttgctctatcttattcttgaatatttggacattgaagttttctttgttaagttgcttcta--attgaatgttgaaacaacctttcttgtacggctctgtttgcactcttaa-cttttgcttttccgggcacttttaatatttaccgtataatgactgtgtagcctgctgtactcatattgtcctcatatatgcagAATAATCTCCATGAACTGTGGGCTCTTCTAAATTTTCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                     || || |    |  |||  ||    ||| || ||          | | || |  |  |||     ||| | ||  |  ||||| |  |  |  |    | || | ||||    |||||||||||||||||  | ||||| || ||||||||  | ||||||||  | ||||| || || ||||| ||||| || ||||||||||||||||| ||||
---------------------ttttttttcttttcgtgttccttagaca-tgctt---------cttactatc--ttctgtacttgatttgctt--gagttaatattgtattcatttcatatgtttctac--tacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 7
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                                                                      ||    ||||||  |  |   | |||  ||||  ||  |||             |  || |   ||||| || || || ||||| ||||| ||| | |||||  | || || ||||| ||||||||||| || |||||||| || |||||||| |||||||| ||||
------------------------------------------------------------------gtacaagatagttgtga-acgtgcttatttattttaccctttttccttgttttcccatttttataccacagAACAACCTGCACGAGCTGTGGGCGCTCTTGAATTTTCTCCTGCCCGAAATCTTTAGCTCTGCTGAGACCTTTGACGAGTGGTTTCAGATTTCTGGAGAAA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 7
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgt-catattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                                                                      ||    ||||||  | |  |  ||||   |||| |||  |||             |  || |   ||||| || || || ||||| ||||| ||| | |||||  | || || ||||| ||||||||||| || |||||||| || |||||||| |||||||| ||||
------------------------------------------------------------------gtacaagatagttgtgaacgtgcttatttt-attttactctttttccttgttttcccatttttataccacagAACAACCTGCACGAGCTGTGGGCGCTCTTGAATTTTCTCCTGCCCGAAATCTTTAGCTCTGCTGAGACCTTTGACGAGTGGTTTCAGATTTCTGGAGAAA

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|19436129|gb|BM952539.1|BM952539
EST:     GGATTTACAACCCTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAG                         AATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATA
genomic: GGATTTACAACACTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAGgtaggcttct ... tacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATA




















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: 471

TGAAGCTCACCGGATAAAAAATGAGAATTCTCTTCTATCGAAGACTATGAGGATTTACAACACTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAGgtaggcttct ... tacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

TGAAGCTCACCGGATAAAAAATGAGAATTCTCTTCTATCGAAGACTATGAGGATTTACAACACTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAGgtaggcttct ... tacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

TGAAGCTCACCGGATAAAAAATGAGAATTCTCTTCTATCGAAGACTATGAGGATTTACAACACTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAGgtaggcttct ... tacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

TGAAGCTCACCGGATAAAAAATGAGAATTCTCTTCTATCGAAGACTATGAGGATTTACAACACTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAGgtaggcttct ... tacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
                    atctgat  putative branch site (score: 199)
     ttagttttt  TA-rich tract