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

gtaagtactgttattaaattaacattaaacgttcactttgtcttgtgcaactatttttttacttttgcatatacacattcttgccttttataatctaattagtactcaatacaattgcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATATTGGACAAGGAGAAGTTGTGGACCATCTATGGAG

Basic information

species	Zea mays
transcript	GRMZM2G020775_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G147041_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g49320.1 (Oryza sativa), 3'ss of exon 3

gtaagtactgttattaaattaacattaaacgttcactttgtcttgtgcaactatttttttacttttgcatatacacattcttgccttttataatctaattagtactcaatacaattgcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATATTGGACAAGGAGAAGTTGTGGACCATCTATGGAG
||||| ||     |  ||||||  ||  | |  |  ||   |||      ||| | |   |  |   ||| |    | |  |      |||||   | |   | || |    ||||||| || ||||||||||||||||  |||||||||||||||||| ||||| |||||||||||||||||||||||  | |||||||||||||||||
gtaagaacgaaagtgtaattaaatttgtatgcaccattgaacttaatgctctaatgt---agctcctcattt---taattatatgcactataactcagtgcttgcttacctaaattgcatttgtagGTATGGTTATGTTTCTCCTGATGATGTGCCTGTCTTGCTACATAAACATATTGGACAAGGAGAGATCGTGGACCATCTATGGAG

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|67023914|gb|CO452663.1|CO452663

EST:     ACGTCATCATTTTCAGTTCTGATGCCAAGGGGAGAAGTGACTGGTCATTG                         GTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT
genomic: ACGTCATCATTTTCAGTTCTGATGCCAA-GGGAGAAGTGACTGGTCATTGgtaagtactg ... gcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT

EST: gi|74232969|gb|DT640883.1|DT640883

EST:     AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTG                         GTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT
genomic: AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTGgtaagtactg ... gcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT

EST: gi|19057851|gb|BM736518.1|BM736518

EST:     AACGTCATCATTTTCAGCTCTGATGCCAAGGGAGAAGTGACTGGTCATTG                         GTATGGCTATGTTGCTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT
genomic: AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTGgtaagtactg ... gcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT

EST: gi|211389154|gb|FL356157.1|FL356157

EST:     AATGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTG                         GTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT
genomic: AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTGgtaagtactg ... gcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT

EST: gi|211066679|gb|FL084209.1|FL084209

EST:     AATGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTG                         GTATGGTTATGTT
genomic: AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTGgtaagtactg ... gcaattatagGTATGGTTATGTT

EST: gi|22490761|gb|BU050684.1|BU050684

EST:     AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTG                         GTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT
genomic: AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTGgtaagtactg ... gcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT

EST: gi|211059299|gb|FL363871.1|FL363871

EST:     AATGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTG                         GTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTTCTGCATAAACATAT
genomic: AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTGgtaagtactg ... gcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT

EST: gi|19058328|gb|BM736995.1|BM736995

EST:     AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTG                         GTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT
genomic: AACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTGgtaagtactg ... gcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATAT

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: 116

AGGTGGCTGTCAGTGCATGCTCACACGTGGGAGGTCATAAGTATGCAGGAAACGTCATCATTTTCAGTTCTGATGCCAAGGGAGAAGTGACTGGTCATTGgtaagtactg ... gcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATATTGGACAAGGAGAAGTTGTGGACCATCTATGGAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 204

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 210

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tacacattcttgccttttataatctaattagtactcaatacaattgcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATATTGGACAAGGAGAAGTTGTGGACCATCTATGGAG

                     atctaat  putative branch site (score: 210)
              ttttataatctaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtactgttattaaattaacattaaacgttcactttgtcttgtgcaactatttttttacttttgcatatacacattcttgccttttataatctaattagtactcaatacaattgcaattatagGTATGGTTATGTTGTTCCTGATGATGTGCCTGTTTTGCTGCATAAACATATTGGACAAGGAGAAGTTGTGGACCATCTATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT