ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttcctatatgttttctatatcagaagtttggtcagcaggatcattgaattgttctaatcatatcaattttgtttcctacag

Basic information

species	Zea mays
transcript	GRMZM5G856084_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g26914.1 (Oryza sativa), 5'ss of exon 7

GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttcctata-tgttttctatatcagaagtttggtcagcaggatcattgaattgttctaatcatatcaattttgttt-cctacag
||| |||||||||||||||||||||| ||||||||||||||||||||||| ||| ||||||||||||| ||||| |||||||| |||||||||| | |||| || |  || ||||| || |||||| || | ||  ||  |  | ||  ||| || |||||    || |||
GTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGAgtgagtgttcctagaatgttgtccaattctgaagtatgatcagcatgacctttatatgatattgattgtatgaaatttgtgaatctgcag

upper sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S386_29V6.1 (Physcomitrella patens), 5'ss of exon 6

GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGG-----CATG-GGCACAGGAgtaagtgttcctatatgttttctata----tcagaagtttggtcagcaggatcat-tgaattgttctaatcatatcaattttgt---ttcctacag-----------------------------
||||| |||||||||||||||||||| || ||||| | || ||| ||||| ||||| || ||||||||     || | || || || ||||||   |   ||| | ||| | |    |    | ||| |  ||| | | | | || |||          | | ||  |||    |||  ||                               
GTTCTCTCTGATGATGAGAAGCGATCAATTTATGACAGATTTGGTGAAGCTGGTCTTAAAGGTGCTGGAGGTGCAGGAGGGACTGGGgtaagttacctcgtatatattccagaggcgtgtatatttttgctagctgtaacctgtgtattacatcccctgttttaacattggaagttctcacttttttttcttctgtgcactgcttgatgaag

upper sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 7
lower sequence: EFJ10769 (Selaginella moellendorffii), 5'ss of exon 5

GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAG-GAgtaagtgttcctatatgttttctatatcagaagtttggtcagcaggatcattgaattgttctaatcatatcaattttgtttcctacag
||||||||||||||||| || ||||| ||||| ||||||||||| ||||| ||| |||| || |||||    ||  |||  |||   ||  | |   |||| | |   | |     ||| |      | |||                                      
GTTCTGTCTGATGATGATAAACGATCCATCTACGATAAATATGGTGAAGCTGGTTTGAAAGGAGCTGGAGCTGGAGCAgtaagtctttgaactttggtgttattttccttactc-cttgcttgctttgctcag-------------------------------------

upper sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 7
lower sequence: EFJ07566 (Selaginella moellendorffii), 5'ss of exon 4

GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAG-GAgtaagtgttcctatatgttttctatatcagaagtttggtcagcaggatcattgaattgttctaatcatatcaattttgtttcctacag
|||||||||||||| || || ||||| ||||| ||||||||||| ||||| ||| |||| || |||||    ||  ||| ||||   ||  | |   |||| | |   | |     ||| |      | |||                                      
GTTCTGTCTGATGACGATAAACGATCCATCTACGATAAATATGGTGAAGCTGGTTTGAAAGGAGCTGGAGCTGGAGCAgtgagtctttgaactttgttgttattttccttactc-cttgcttgctttgctcag-------------------------------------

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|61119026|gb|DN559987.1|DN559987

EST:     ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA                         GATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT
genomic: ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttc ... tttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT

EST: gi|148950667|gb|EC896255.2|EC896255

EST:     ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA                         GATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT
genomic: ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttc ... tttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT

EST: gi|148955679|gb|EC901358.2|EC901358

EST:     ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA                         GATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT
genomic: ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttc ... tttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT

EST: gi|211525859|gb|FL340350.1|FL340350

EST:     ATGATAAATATGGAGAAGCAGGTCTGAAAGGTGCTGGCATGGGCACAGGA                         GATTACTCAAACCCGTTTGATCTCTTTGAG-CCCTGTTTGAAGG-TTTG
genomic: ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttc ... tttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTG

EST: gi|149051735|gb|EE155859.2|EE155859

EST:     ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA                         GATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT
genomic: ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttc ... tttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT

EST: gi|211152737|gb|FL348042.1|FL348042

EST:     ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA                         GATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGG
genomic: ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttc ... tttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGG

EST: gi|71769003|gb|DR966940.1|DR966940

EST:     ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGA                         GATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT
genomic: ATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttc ... tttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 101

GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttc ... tttcctacagGATTACTCAAACCCGTTTGATCTCTTTGAGTCCCTGTTTGAAGGGTTTGGTGGAATGGGTGGAATGGGGGGTGGCCGTGCTGCTCGGAACAGACCAATGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 72

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 134

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTGTCTGATGATGAGAAGCGATCGATCTATGATAAATATGGAGAAGCAGGTCTGAAGGGTGCTGGCATGGGCACAGGAgtaagtgttcctatatgttttctatatcagaagtttggtcagcaggatcattgaattgttctaatcatatcaattttgtttcctacag

- - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG