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

gtcggatttgttgcattagatgagaaaaaaattaagtgttgaacggttctttatacctttttttatttgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG

Basic information

species	Zea mays
transcript	GRMZM2G079196_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 4

gtcggatttgttgcattagatgaga-aaaaaattaagtgttgaacg---gttctttatacctt-tttttatttgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG
||    ||| |||| |||    |   | ||  ||| ||    || |   ||||||||||||||  | || ||||||| ||||||||||||||| ||||||||| ||||||||||||||||||||||||| || || ||||| || || |||||||||
gttcagtttcttgccttatccaaattagaattttatgtaccaaaagattgttctttataccttgctattctttgctgcgcagAGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAG

upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 4

---------gtcggat--ttgttgcat--tagatga----gaaaaaaatt-aagtgttgaacg-gttctttatacctt-tttttatttgc---tgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG
         ||  |||  ||||   ||  |||||      || |   ||  || |  || ||   |||   | |  || |||||||||     | | ||||| |||||||||||||||||||||||  | || ||| | ||||||||||| || || || ||||  |||| ||| 
tgcaccagagttagatccttgtaagataatagatctttttgacatgtatcgaaatcctgtacatattcagaagattttgtttttatttttgcatttacagAGGTTATGGTTCAAGACAAACTTGAAATTGTGTAAATTGTGGTTTGATATGGGAGAATATGGTCTTATGAACAAA

upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 4

-------------------------gtcggatttgttgcattagatgagaaaaaaattaagtgttga-acggttctttatacctttttttatttgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG
                         |  | |    ||||| | | |  |      ||||||  || |    ||| || | |     |||  || | ||||||||||||||||||||| || ||||||||| | |||||| | ||||||||||| || || || ||||| |||| ||| 
acaccacactttaccacttgcactaggtgtaacacttgcaatcgtttggtctg--attaagcatttatgtagtttttcagatagcattt-gttggttgtgcagAGATTATGGTTCAAAACGAACTTGAAGTTGTGCAAATTGTGGTTTGATATGGGAGAATATGGTCGAATGAACAAA

upper sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 4

----------------------gtcggatttgtt-gcattagatgagaaaaaaattaagtgttgaacggttctttatacctttttttatttgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG
                         | |  || |   |   | |  |   |    ||  | || |    ||  || |   ||||||  |||    ||||||| |||||||||||||||||||||||| | || ||| | ||||||||||| || || || ||||| ||||  |||
taaaggatttaaactttggaaccctgtacctgctcataaatgttttgttgatttctatttttttatttttttattttttattttttcgtttttattgcagAGGTTATGGTTCAAGACAAACTTGAAGTTGTGTAAATTGTGGTTTGATATGGGTGAATATGGTCGAATGAATAAG

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|211292183|gb|FL267075.1|FL267075

EST:     AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAANAAGCGAAAAATGAG                         AGATTATGGTTCAAGACAAACTTGAAGC
genomic: AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGC

EST: gi|211287913|gb|FL267057.1|FL267057

EST:     AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAT                         AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA
genomic: AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA

EST: gi|211294335|gb|FL267099.1|FL267099

EST:     AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAG                         AGNAT-ATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATAT
genomic: AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAG-ATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATAT

EST: gi|76015005|gb|DT942175.1|DT942175

EST:     AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAG                         AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA
genomic: AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA

EST: gi|31353952|gb|CD438309.1|CD438309

EST:     AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAG                         AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA
genomic: AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA

EST: gi|193502120|gb|AM937931.1|AM937931

EST:     AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAG                         AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGGTATA
genomic: AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA

EST: gi|211290048|gb|FL267064.1|FL267064

EST:     AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAG                         AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA
genomic: AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA

EST: gi|32932790|gb|CF037602.1|CF037602

EST:     AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAG                         AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA
genomic: AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA

EST: gi|32931205|gb|CF036017.1|CF036017

EST:     AAGAGTTCTACCAGACAACACTGAAGGCGCTTGAAGAAGCGAAAAATGAG                         AGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA
genomic: AAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATA

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: 174

CATAATGGATTTTGTTTCTGGATCAGCTAGTCAGAATTTTACTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttg ... tgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG

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

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 166

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agaaaaaaattaagtgttgaacggttctttatacctttttttatttgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG

                        ttctttataccttttt  CT-rich tract
                        ttctttataccttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggatttgttgcattagatgagaaaaaaattaagtgttgaacggttctttatacctttttttatttgctgtgcagAGATTATGGTTCAAGACAAACTTGAAGCTTTGCAAAATTTGGTTTGATATAGGCGAGTACGGTCGCATGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG