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

gtatgatcacttccaattttacattgagctctggttggcagttagcacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT

Basic information

species	Zea mays
transcript	GRMZM2G157462_T01
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9

gtatgatcacttccaattttacattgagctctg--gttggcagttagcacatgatt---aaacac-----atttctctcc-acacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
||| |||    |||| ||| |   | ||  ||    |  |   ||  | |||  ||    |||||     | |  ||||  |||   ||||||||||||||||| |||||||||||||| ||  ||||||||||||||||||||||||| ||||| ||||| |||||| |||| ||||||||||||||||
gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9

-------------------------gtat-gatcacttccaattt--tacattgagctctggttggcagtta--gcacatgattaaacacatttctctccacacaat--agATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
                          ||| | | |  |  |||||  | ||||    |||  ||| || ||   |  | || ||  | |      | |   |  | |  |||||||| | ||||||||||| |||||||| ||| | || |||||||||||||| |||||||||||||| |||   || || ||| |||||||||||||||
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctc-ttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9

-------------------------gtat-gatcacttccaattt--tacattgagctctggttggcagttag--cacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
                          ||| | | |  |  ||| |  | |||     |||| ||| || || |    | || ||  | |  | ||  |         |||||||| | ||||||||||| |||||||| ||| |||| |||||||||||||| |||||||||||||| |||   || || ||| |||| ||||||||||
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctg-ttgacacttggggtgcttgcttctatat-tctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9

------------gtatgatcacttccaattttacat-tgagctctggttggcagttagcacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
             | |     | || |||| || |    ||    || |      | |    |||   |     ||||            |||| || ||||| || |||||||||||||| ||| | |||||||||||||||||||||||||| ||||||||||  || || ||  |||| || || ||| 
gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattgattttccaattgttt--cagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9

--gtatgatcacttccaattttacattgagctctggttggcagttagcacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
  |  ||    ||||     | |  ||  || |  |       ||   || |||||   || |  | |||         || |||| ||||| ||||||||||||||||| ||| | |||||||||||||||||||||||||| || ||||| || || || ||  |||| || || ||  
gtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgtca-aaatatctttgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 9

-----------gtatgatcac-ttccaatttta----cattgagctctggt-tggcagttagcacatgattaaacacatttctctccacacaata---gATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
            | |  |||| |||||| |||     | || |  | || | | | |        ||  ||    |  || || | ||    |||   ||||||  | |||||||||||||||||||| ||| | ||||||||||| ||||| || || ||  |||||||||| || |||||  |||| || |||||||
gtatggttctcttttattcacattccaacttttgtgccttttaaatatgttgttgtaaggcctttattgtttgcaatgttccttttcaattgataccagATTGTGCTAGAAGCAGATGGTTATCAACCTTATCTTATATCTCCAGAAAAAGGTTTAAGGTCTCTAATAAAAATTGTCCTGGAGCTGGCGAAAGAGCCAT

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9

------------gtat-gatcacttccaattttacattgagctctggttggcagttagcacatgatta----aacacatttctctccacacaat---agATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
            || | | ||  |  |||||||| | |    | ||| |     ||      | ||||     |   ||||  | |||     |   ||||||| || ||||| |||||||||||||||||| | |||||||| |||||||| |||||||| |||||||||   ||  ||||  | ||||| |||||||
gtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ37003 (Selaginella moellendorffii), 3'ss of exon 9

gtatgatcacttccaattttacattgagctctggttggcagttagcacatgatta-aacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
                               | |  |   || |  ||  | ||  ||     ||     |  |  | || | ||  | ||||| ||||| ||||||||||||||| | ||||||||||||||| || ||    |  ||  || ||  || ||| | || || || ||  
-----------------------------gttagcagcatgtgactacgggtttttaatgttctttctggcttatcacagGTGGTTCTTGAAGCGGATGGGTATCAACCATATTTGCTCTCTCCAGAGAAAGGGCTGCGAGAGCTTGTACGAAGAGCTCTCGAACTTGCTAAAGATCCTG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ33653 (Selaginella moellendorffii), 3'ss of exon 9

gtatgatcacttccaattttacattgagctctggttggcagttagcacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
                      | | |||      || |     |       || ||     ||     |  |  | || | ||  | ||||| ||||| ||||||||||||||| | ||||||||||||||| || ||    |  ||  || ||  || ||| | || || || ||  
--------------------gtagttagcagcatgtgacgacgggtt-----tttaatgttctttctggcttatcacagGTGGTTCTTGAAGCGGATGGGTATCAACCATATTTGCTCTCTCCAGAGAAAGGGCTGCGAGAGCTTGTACGAAGAGCTCTCGAACTTGCTAAAGATCCTG

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|211286766|gb|FK982432.1|FK982432

EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA

EST: gi|9254689|gb|BE345157.1|BE345157

EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA

EST: gi|211286763|gb|FK982429.1|FK982429

EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA

EST: gi|87155357|gb|DY400146.1|DY400146

EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA

EST: gi|30306992|gb|CD001665.1|CD001665

EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA

EST: gi|22472855|gb|BU037335.1|BU037335

EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA

EST: gi|211132359|gb|FK982426.1|FK982426

EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA

EST: gi|31361304|gb|CD445661.1|CD445661

EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA

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), 48 (downstream exon)
Score: 234

ATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 254

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 227

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgagctctggttggcagttagcacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT

                                   catttctctcc  CT-rich tract
                        atgattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatcacttccaattttacattgagctctggttggcagttagcacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG