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

...ttctttccatctgatgtacgactctttgctattcttcagcttagtatttacttggggatctgagtttaaatgccagagaatgattttattttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA

Basic information

species	Zea mays
transcript	GRMZM2G101438_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g52420.1 (Oryza sativa), 3'ss of exon 3

ttctttccatctgatgtacgactctttgctattcttcagcttagtatttacttggg--gatctgagtttaaatgccagagaatgattttattttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA
  |||| |||||||| || | ||||      ||||    ||||  ||   || |||  |     |  | || || || ||| ||||||  | ||||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||| | |||||||||||||| ||||| || ||||||||||| || |  |||||||
--cttttcatctgatatatgtctctgcttgtttctcagacttaccatactctagggatgtataaaactcaagtgtcaaagactgatttgttcttattgacagCCAGGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGA

upper sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g52420.2 (Oryza sativa), 3'ss of exon 3

ttctttccatctgatgtacgactctttgctattcttcagcttagtatttacttggg--gatctgagtttaaatgccagagaatgattttattttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA----
       |||||||| || | ||||      ||||    ||||  ||   || |||  |     |  | || || || ||| ||||||  | ||||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||| | |||||||||||||| ||||| || ||||||||||| || |  |||||||    
------tcatctgatatatgtctctgcttgtttctcagacttaccatactctagggatgtataaaactcaagtgtcaaagactgatttgttcttattgacagccagGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGT

upper sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 3

ttctttccatctgatgtacgactctttgctattcttcagctta---gtatttacttggggatctgagtttaaatgccagagaatgattttattt-tattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA
   ||   |  || |  |  | | | |   ||| | | | ||    || |||| ||    |    |  ||   |      |   | ||| | || | |||||||||||||||||| || |||||||||||  ||||||| ||||||||||||||||||||||| ||||| || || ||||| || ||| || | |  || ||||
---ttatgaagtgtta-ataattttgtataattatactgattttatgtttttattttaaaagaaaaagttgtttttttatgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA

upper sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT4G37040.1 (Arabidopsis thaliana), 3'ss of exon 3

ttctttccatctgatgtacgactctttgctattcttcagcttagtatttacttggggatctgagtttaaatgccagagaatgattttattttatt-gacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA
              || | ||   |||  || | |    || |   |||   |   | |||   || |     || |   | ||| | || |||| | ||||||||| |||| ||||||||||| ||| ||||||| ||| | ||||| ||||| |||||||| |||||||| |||||||||||| | || | ||| || |
-------------gtg-aggaaagttttatactttctgtctcat--tttgaataatgctcta--ttaattcatcataattttattcttttctatttggcagCCAGGCGTAACCACTGATGAAATCGATGAAGCAGTTCACAATATGATTATTGAGAATGGAGCTTATCCTTCGCCTCTTGGTTATGGAGGTTTCCCGAAAA

upper sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0031g00820.t01 (Vitis vinifera), 3'ss of exon 3

--ttctttccatctgatgtacgactctttgctattcttcagcttagtatttacttggggatctga-gtttaaatgccagagaatgattttattttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA
          ||  |||| |  |||  ||||   |     |||||| |   |        ||| | || | ||        |||  ||   ||  |||| ||||||||||||| ||| |||||||||||  ||||||| ||||||||||| ||||||||||| || || ||||| || || || ||| ||||||  |||||||
agggaaggaaataagatggaatactgattgcatatacatggcttaggacgcaggcacatttcttatgtctgaaaatttt--aattgttgc-ttcaattggcagCCAGGCATAAAGACGGATGAAATTGACGAAGCAGTTCACCAAATGATTATTGATAATGGTGCGTACCCTTCCCCCCTAGGCTATGGTGGATTTCCAAAGA

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|211227811|gb|FL170954.1|FL170954

EST:     CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAG                         CCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCA
genomic: CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCA

EST: gi|148995508|gb|EE034697.2|EE034697

EST:     CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAG                         CCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT
genomic: CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT

EST: gi|76912468|gb|DV164746.1|DV164746

EST:     CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAG                         CCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT
genomic: CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT

EST: gi|78075681|gb|DV504115.1|DV504115

EST:     CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAG                         CCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT
genomic: CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT

EST: gi|101399011|gb|EB821378.1|EB821378

EST:     CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAG                         CCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT
genomic: CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT

EST: gi|78082005|gb|DV510417.1|DV510417

EST:     CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAG                         CCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT
genomic: CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT

EST: gi|71436246|gb|DR817296.1|DR817296

EST:     CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAG                         CCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT
genomic: CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT

EST: gi|116819988|gb|EC863161.1|EC863161

EST:     CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAG                         CCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT
genomic: CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT

EST: gi|76289409|gb|DV028977.1|DV028977

EST:     CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAG                         CCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT
genomic: CTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATT

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), 42 (downstream exon)
Score: 33

TAATGGACCTGAAATACATGATGAGAACGGGATCGAGTGCATGAGAGCTTCTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat ... ttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 41

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 21

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 28

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atttacttggggatctgagtttaaatgccagagaatgattttattttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA

                                      ttttatttt  CT-rich tract
                             agagaatgattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttccatctgatgtacgactctttgctattcttcagcttagtatttacttggggatctgagtttaaatgccagagaatgattttattttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - ctgatgt
- - - - - - - - - - - - - tgctatt
- - - - - - - - - - - - - - - - -cttcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcca