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

...tggtcatttcttttagcatggtagtgatcgtgcagatagatgtacaatattcctttctccagagctatactctatgacctactataccctgttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATG

Basic information

species	Zea mays
transcript	GRMZM2G010146_T03
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G010146_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g33020.1 (Oryza sativa), 3'ss of exon 2

----------------------------------tggtcatttct--tttagcatggtag------tgatcgtgcagatagatgtacaatattcctttctccagagctatactctatgacctactataccctgttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATG
                                  |   ||||  |  | | ||||| |        || | |  ||||  | |||  ||||    ||  |||| | | |||   | | ||  ||  |||| |  || |||||||||| ||||||||||||||||||||||||||||| || ||| |||| ||||||||||||||||||||||||||||| ||||||||||||||| |||| |
gttagtcaatttgtttcatctcctgccttccagttttccattcttaatatggcatgattttatctttgctggaacagaatgttgtttaataccatttgttccaaaac-atatcat-tcactgacactaccattatg-tgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAGCATATCTACAACCTATATGTGGAATATGTTGTAAAAAATCCTTTGTACG

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|71425314|gb|DR806606.1|DR806606

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|71302504|gb|DR787370.1|DR787370

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|93284352|gb|EB676616.1|EB676616

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|91872814|gb|EB402771.1|EB402771

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|78083968|gb|DV512361.1|DV512361

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|94477699|gb|EB706657.1|EB706657

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|76292671|gb|DV032239.1|DV032239

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|148930227|gb|EC872669.2|EC872669

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|71302502|gb|DR787369.1|DR787369

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|76930391|gb|DV172363.1|DV172363

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|71316462|gb|DR794908.1|DR794908

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|78118287|gb|DV536673.1|DV536673

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|71436637|gb|DR817687.1|DR817687

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|101393644|gb|EB818754.1|EB818754

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|74238223|gb|DT646137.1|DT646137

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|148932965|gb|EE285816.2|EE285816

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|211038846|gb|FL245342.1|FL245342

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|71434336|gb|DR815386.1|DR815386

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|71436489|gb|DR817539.1|DR817539

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCCAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|76930392|gb|DV172364.1|DV172364

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|76918988|gb|DV167546.1|DV167546

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|14243987|gb|BG841705.2|BG841705

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

EST: gi|148944695|gb|EC889832.2|EC889832

EST:     AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAG                         CTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG
genomic: AGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAG

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: 85

TCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTTACGGAGAGCCCTTCTGGTATAAAGgttagtattg ... gttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 75

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 61

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 47

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aatattcctttctccagagctatactctatgacctactataccctgttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATG

                                         ccctgtt  CT-rich tract
                                  tactata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtcatttcttttagcatggtagtgatcgtgcagatagatgtacaatattcctttctccagagctatactctatgacctactataccctgttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATG

- - - - - - - -gcatggt
- - - - - - - - - - - - - - cgtgcag
- - - - - - - - - - - - - - - - - - - gatgtac