ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacag

Basic information

species	Zea mays
transcript	AC233979.1_FGT009
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC233979.1_FGT009 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G41040.1 (Glycine max), 5'ss of exon 4

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacag
||||| |||||||||| || ||  | ||||| |||||||| | |||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||||||||   |    ||   |  |  |||     |||   |       ||   | ||| ||         | | | | | |||
ATGTGCACCATCCTTATAAACCTCTTGTTGAGGCAATAAAGAAATTCAAAGTTGCTCAAAATGCCCTTGCTCAAGTTGCGTGGAATTTTGTAAATGATGGgtatgaagattacacaaatttttgttaaggccagtggcctttg---atttttctttcctgaaatgaggatgtgatatgcag

upper sequence: AC233979.1_FGT009 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G35010.1 (Glycine max), 5'ss of exon 4

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaaattactctt-------------cctcattacaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacag
||||  | ||||| || || ||  | || ||||| ||||| |  || || |||||  | ||||| ||||| |||||||| ||||| ||||| ||||||||||||| |    || |  ||             | |||||  || |  |  |    ||| ||   | || || || | |  |||| ||  | |||
ATGTTCAACATCCGTATAAACCTCTTGTGGAAGCCATAAAGAAGTTTAATGTTGCGAAGAATGCCCTTGCACAAGTTGCATGGAACTTTGTTAATGATGGgtatgatttggttgccatttgtttgaatttaacttcattg-aatttattttttttaaatatatttgttcac-acac-tggaaagtggctttcag

upper sequence: AC233979.1_FGT009 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G17960.1 (Glycine max), 5'ss of exon 4

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacag
||||| | |||||||| || ||  | ||||| |||||||| | |||||| || ||||||||||| || ||||||||||| ||||||||||| |||||||||||||  || ||||| |    |  ||  |        |   |    ||   | ||| ||     |   | | | | | |||
ATGTGCATCATCCTTATAAACCTCTTGTTGAGGCAATAAAGAAATTCAAAGTAGCTCAAAATGCCCTAGCTCAAGTTGCGTGGAATTTTGTAAATGATGGgtatg--aagattacacaattttttttaaggcgagtgtggcctttgatttttctttcctgaaattaggatgtgatatgcag

upper sequence: AC233979.1_FGT009 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G02860.1 (Glycine max), 5'ss of exon 5

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaaattac--tcttcctcattacaa--atagtaatccac-----aaacatccctatttac-tacgccttaaaaggggtgtacag
||||  | ||||| || || ||  | || ||||| ||||| |  || || |||||  | ||||| ||||| |||||||| ||||| ||||| ||||||||||||| |    || |  | |   | | |  ||   |    ||  |      ||| ||   |  | ||  ||     ||||| ||  | |||
ATGTTCAACATCCATATAAACCTCTTGTGGAAGCCATAAAGAAGTTTAATGTTGCGAAGAATGCCCTTGCACAAGTTGCGTGGAACTTTGTTAATGATGGgtatgatttggttgcaatttgtttgaatttaactgtgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcag

upper sequence: AC233979.1_FGT009 (Zea mays), 5'ss of exon 4
lower sequence: AT5G45190.1 (Arabidopsis thaliana), 5'ss of exon 5

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgct--aaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgcctta------aaaggggtgtacag
||||  | |||||||| || ||| |||| ||||||||||| | ||| |||||||| || ||||||||||| |||||||| ||||||||||| ||||||||||| | |  | || || |       |   |    | |||| |           ||||| |  |  | ||      |||| ||  | |||
ATGTTTATCATCCTTATAAACCCCTGGTAGAAGCAATAAAGAAATTTAAGGTTGCACAGAATGCACTTGCCCAAGTTGCATGGAATTTTGTTAATGATGGgtacgttcaagaactatttccttctaaagcttccaataattctatgtgccttgtattttcgtcttcatacaatgaaaagtggcttgcag

upper sequence: AC233979.1_FGT009 (Zea mays), 5'ss of exon 4
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 5'ss of exon 4

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAAT---GCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaaattactcttcc----------------------tcattacaaatagtaa----tccacaaacatccctatttact-acgc-cttaaaaggggtgtacag
   |||  ||     | ||  |   |    |    ||     |  ||| ||||||    |||   || |||||||||||||| ||||||||||||||||||||||||| | ||  | || || |                       |||| ||||| ||      ||| |       | | || ||| || | ||  |||| ||  | |||
--TTGAGGCAATGAAAAAATTCAAAGCCGCACAGGATGCTCTTGCTCA-GGTTGCATGGAATTTTGCTCTTGCTCAAGTTGCATGGAATTTTGTCAATGATGGgtatgattaagatgctttttcatgtctctcttttttgatagttccatttcaaatggtctctcttcctctctttctcttcttcactcacacactggaaagcggcttgcag

upper sequence: AC233979.1_FGT009 (Zea mays), 5'ss of exon 4
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 5'ss of exon 4

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacag
||||| ||||||| || || ||| | || || |||||||| | ||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||| |    || ||  |  |  |||   |   || |   |   | ||| | |   ||   |||   ||| ||  | |||
ATGTGCACCATCCATATAAACCCCTTGTAGAGGCAATAAAGAAATTCAAGGTTGCTCAAAATGCCCTTGCTCAAGTTGCTTGGAATTTTGTCAATGATGGgtatgatggg-ttgcttcttttttttatgcacgttattgttctttcttccttctcatcttgacctgggaagcggcatgcag

upper sequence: AC233979.1_FGT009 (Zea mays), 5'ss of exon 4
lower sequence: EFJ27727 (Selaginella moellendorffii), 5'ss of exon 4

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaaat-tactctt-----cctcattacaaatagtaatccacaaacatccctatttactacgccttaa---aaggggtgtacag-------------------
| ||  ||||||| ||||  ||  |||| |  || |||||||  ||||| ||  ||||| |||| || ||||||||||| ||||| ||||||||||||||||| |||       ||   |     | ||| |    |  | | |     |       |  || |  | | || |    | |||  |  ||                   
ACGTTCACCATCCATACAGACCGCTGGTGGCCGCCATAAAAAAGTTCAACGTCTCTCAACATGCGCTGGCTCAAGTTGCGTGGAACTTTGTCAATGATGGgtaagctctcgcacaccagtaggaacttcagtctcgactggagtgttggagtccgtgttgtttcatcactttgatgagatgggaatgaagcagtggaagggatgtgcag

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|16925641|gb|BM078709.1|BM078709

EST:     GTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGG                         GCTCCGCACTTCACTTTGNCCTGCA-TTTAAACCGCACCATATTGCGGCTG
genomic: GTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaa ... gggtgtacagGCTCCGCACTTCACTTTG-CCTGCAATTTAAACCGCACCATATTGCGGCTG

EST: gi|32799767|gb|CD952003.1|CD952003

EST:     GTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGG                         GCTCCGCACTTCACTTTGCCTGCAATTTA
genomic: GTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaa ... gggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTA

EST: gi|116826111|gb|EC869868.1|EC869868

EST:     GTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGG                         GCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGG
genomic: GTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaa ... gggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGG

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: 180

ATGTGAACCATCCTTACAAGCCCTTGGTTGAAGCAATAAAAATATTCAAGGTTGCTCAAAATGCACTTGCTCAAGTTGCCTGGAATTTTGTCAATGATGGgtatgctaaa ... gggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 151

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161