ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgctaaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT

Basic information

species	Zea mays
transcript	AC233979.1_FGT009
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4

----------------gtatgctaaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT
                 | || |  ||||   |||| |      || |  |  |    ||| ||   | || || || | |  |||| ||  | ||||||  | || || || |||||||||||||| || || ||||||||||| ||||| || ||||| ||||| |||||  | ||||| |||||||||||||||
gtatgatttggttgccatttgtttgaatttaacttcattg----aatttattttttttaaatatatttgttcac-acac-tggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

upper sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4

gtatgctaaaattac--tcttcctcattacaaatagtaatccac-----aaacatccctatttac-tacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT
||||| |    || |  | |   | | |  || |    ||  |      ||| ||   |  | ||  ||     ||||| ||  | ||||||  | || || || |||||||||||||| || || ||||||||||| ||||| || ||||| ||||| |||||  | ||||| |||||||||||||||
gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

upper sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 5

gtatgctaaaattac--tcttcctcattacaa--atagtaatccac-----aaacatccctatttac-tacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT
||||| |    || |  | |   | | |  ||   |    ||  |      ||| ||   |  | ||  ||     ||||| ||  | ||||||  | || || || |||||||||||||| || || ||||||||||| ||||| || ||||| ||||| |||||  | ||||| |||||||||||||||
gtatgatttggttgcaatttgtttgaatttaactgtgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

upper sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4
lower sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 5

gtatgct--aaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgcctta------aaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT
||| | |  | || || |       |   |    | |||| |           ||||| |  |  | ||      |||| ||  | ||| || || || || || |||||||||||||| || || |||||||||||||||||||| || || || || ||||| || ||||| ||| | |||||||||
gtacgttcaagaactatttccttctaaagcttccaataattctatgtgccttgtattttcgtcttcatacaatgaaaagtggcttgcagTCTACGGACATCTCTCTGCCTGCAATTTAAGCCTCATCATATTGCGGCTGGTGCAATATTTCTTGCGGCCAAGTTCCTTAAAGTGAAGTTACCATCAGAT

upper sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4
lower sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6

gtatgctaaaattactcttcctca----ttacaaatag---taatccacaaacatccctatttactacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT
||| | ||||| |    |||||       | || ||||   ||     |    ||     | | |      | |||||  |  | ||| || || || ||||| |||||||||||||| || ||||| |||||||| || ||||| || || ||||||||||| || ||||| ||  | |||||||||
gtacgttaaaagtctgtttccttgaaagcttcagatagatctatctgtcttgtattttcttcttcatacaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT

upper sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 4

-------------gtatgctaaaattactcttcct---------cattacaaatagtaa----tccacaaacatccctatttact-acgc-cttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT
             |  |  | |  |  |||||  |         |||| ||||| ||      ||| |       | | || ||| || | ||  |||| ||  | ||||||  | || ||||| |||||||||||||| ||  |||| ||||| || ||||| || ||||| ||||| |||||||||||||| ||||||||||| |||
gtatgattaagatgctttttcatgtctctcttttttgatagttccatttcaaatggtctctcttcctctctttctcttcttcactcacacactggaaagcggcttgcagGCTGAGGACATCACTCTGCCTGCAATTTAAGCCCGACCACATTGCAGCAGGTGCCATTTTCCTTGCTGCCAAGTTTCTCAAAGTGAAGCTTCCATCGGAT

upper sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4
lower sequence: PP1S86_187V6.1 (Physcomitrella patens), 3'ss of exon 5

-----------------gtatgctaaaattactcttcctcat--tacaaatagtaatccacaaacatccctatttactacgccttaa-aaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT
                   ||    | |||| | ||| |  |  |  |||  || | ||||     ||   |      | |        |    ||| ||| || ||||| |||||||||||||||||||| || ||||| || || || || || |||||||||||||| |||||||||||||| || || ||    || 
caagatgccacttttagagatcagcagattaatgttctttgtgctgaaaactgtga-ccactgtagtcggaaaggctaatgtaagggtgattattgtccagACTTCGCACGTCACTTTGCCTGCAATTTAAGCCTCACCACATCGCTGCGGGAGCTATCTTCCTCGCTGCTAAGTTTCTCAAAGTGAATCTGCCGAAGGAG

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

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 146

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

acaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT

                         tatttacta  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctaaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT