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

gtactggatcacatacaacggtataatttcacactgcatacaaccaactgctttctgatagctttttttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGTTTCGGGAATATATGCGATCAGATGGTACCTTTTCATACTTCTTCTCATT

Basic information

species	Zea mays
transcript	GRMZM2G032944_T02
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G032944_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g23169.1 (Oryza sativa), 3'ss of exon 5

gtactggatcacatacaacggtataatttcacactgcatacaaccaactgctttctgatagcttttt-ttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGTTTCGGGAATATATGCGATCAGATGGTACCTTTTCATACTTCTTCTCATT
||| ||   | |   | |   |||  | | | |   |||  | | |    ||| |||| | || ||| || ||| ||| || |||||||||||||||||||||||||||||||| |||||||| || || |||||||| ||||| |||||||| ||| |||||||||||||| ||||
gtaatg---ccctggccatactattgtattatatatcattgatcaataatcttgctgacatctctttattgtattagGACTCTATGACATGACAATGCTTCGGTTTTTACCTCACCAAAGAGTGGGATTCCGGGAATACATGCGCTCAGATGGCACCCTTTCATACTTCTTCACATT

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|211229014|gb|FL455773.1|FL455773

EST:     ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACG                         GTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT
genomic: ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACGgtactggatc ... tttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT

EST: gi|24763644|gb|CA398816.1|CA398816

EST:     CTTCTTTTTAGGGATTACG                         GTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT
genomic: CTTCTTTTTAGGGATTACGgtactggatc ... tttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT

EST: gi|76914811|gb|DV165697.1|DV165697

EST:     ACCAGGCGGCCTTCTTCTTTTTAGGGATTACG                         GTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT
genomic: ACCAGGCGGCCTTCTTCTTTTTAGGGATTACGgtactggatc ... tttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT

EST: gi|149085004|gb|EE174514.2|EE174514

EST:     ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACG                         GTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT
genomic: ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACGgtactggatc ... tttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT

EST: gi|74246084|gb|DT653998.1|DT653998

EST:     ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACG                         GTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT
genomic: ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACGgtactggatc ... tttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT

EST: gi|78124011|gb|DV542395.1|DV542395

EST:     ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACG                         GTCTTTATGACATGACAATGCTTCGGTTTTTACTTCATCAAAGAGTAGGGT
genomic: ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACGgtactggatc ... tttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT

EST: gi|71759527|gb|DR957464.1|DR957464

EST:     ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACG                         GTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT
genomic: ATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACGgtactggatc ... tttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGT

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: 45 (upstream exon), 48 (downstream exon)
Score: 20

TTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAACAATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATTACGgtactggatc ... tttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGTTTCGGGAATATATGCGATCAGATGGTACCTTTTCATACTTCTTCTCATT

Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 26

Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 16

Block sizes: 45 (upstream exon), 39 (downstream exon)
Score: 13

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tataatttcacactgcatacaaccaactgctttctgatagctttttttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGTTTCGGGAATATATGCGATCAGATGGTACCTTTTCATACTTCTTCTCATT

                               ttctgat  putative branch site (score: 13)
                                        ctttttttat  putative PPT
                                    atagctttttttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactggatcacatacaacggtataatttcacactgcatacaaccaactgctttctgatagctttttttatatcagGTCTTTATGACATGACAATGCTTCGGTTTTTACCTCATCAAAGAGTAGGGTTTCGGGAATATATGCGATCAGATGGTACCTTTTCATACTTCTTCTCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG