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

...ataagtcgttcttctccacatttggatgttgtcgttttcctttccctggtgcaaactgtttgctttcccacattttctgaatttttgtctactgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTTCATGAGATGAAGTGCTACGTCGGTCCAGACTTCCGCTACCAAGGGGATG

Basic information

species	Zea mays
transcript	GRMZM2G152056_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152056_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g50870.1 (Oryza sativa), 3'ss of exon 3

ataagtcgttcttctccacatttggatgttgtcgt-tttcctttccctggtgcaaactgtttgctttcccacatttt-----ctgaatttttgtctactgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTTCATGAGATGAAGTGCTACGTCGGTCCAGACTTCCGCTACCAAGGGGATG
       | | ||  |    | | ||| |   | | || | | | |||        || | |    ||    |||||     || |||  || |     ||  ||||||||||| |||||  | ||||||||| |||| ||||||||||||||||| ||||||||||| ||||| || |||||||||||||||||| |||| ||||
------tggttttgccattgtattgatatacgcatattacatatgccttacatttcctttctttcgtctgcaatttttgggactaaatcgtttttcgtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTCCATGAGATGAAATGCTATGTTGGTCCAGACTTCCGCTACGAAGGAGATG

upper sequence: GRMZM2G152056_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g00750.t01 (Vitis vinifera), 3'ss of exon 3

-----ataagtcgttcttctc--cacatttggatgttgtcgttttcctttccctggtgcaaactgtttgctttcccacattttctgaatttt-tgtctactgtt-gcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTTCATGAGATGAAGTGCTACGTCGGTCCAGACTTCCGCTACCAAGGGGATG
     ||||  | || |      | || ||| | |  ||  || |  |||| | | |||||    | |  ||||  |    || |||||    ||||     || ||||||||| || ||||||||||| |||||  |||| ||||| ||||| || |||||||||||||||||||||||    ||   ||||   |||   |      
cctgaataaagcattatgtaaggctcaattgaaagaggt--ttctgttttctcagctgcaat---tatagtttctta----ttgtgaatggcgtgtccgtgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTTCATGAGATGAAGTGCTACGTGAACCCGAGCTTCAATTACAGTGATCCAA

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|211308767|gb|FL253751.1|FL253751

EST:     AGGGCCATCAATCCTCATGCCTACCCTGATGGAAACTGTGTTTTGTTCAG                         TGCTGCGGTTGCAATGTGTTCCAAAAGTTGG
genomic: AGGGCCATCAATCCTCATGCCTACACTGATGGAA-CTGTGTTT-GTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGG

EST: gi|18178629|gb|BM379833.1|BM379833

EST:     CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAG                         TGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT
genomic: CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT

EST: gi|32844105|gb|CD983786.1|CD983786

EST:     CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAG                         TGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT
genomic: CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT

EST: gi|211308770|gb|FL253754.1|FL253754

EST:     CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAG                         TGCTGCGGTTGCAATGTGTTCCATAAGT-GGTCGACAACCTGAACCTGTTT
genomic: CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT

EST: gi|18178294|gb|BM379504.1|BM379504

EST:     CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAG                         TGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT
genomic: CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT

EST: gi|211131519|gb|FL443438.1|FL443438

EST:     CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAG                         TGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT
genomic: CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT

EST: gi|211306744|gb|FL253741.1|FL253741

EST:     CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAG                         TGCTGCGGTTGCAATGTG
genomic: CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTG

EST: gi|211143970|gb|FL467014.1|FL467014

EST:     CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAG                         TGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT
genomic: CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT

EST: gi|211306745|gb|FL253742.1|FL253742

EST:     CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAG                         TGCTGCGGTTGCAATGTGTTCCATAAGTYGGTCGACAACCTGAACCTGTTT
genomic: CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTT

EST: gi|211306750|gb|FL253747.1|FL253747

EST:     CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAG                         TGCTGCGGTTGCAATGTGTTCCATAAG
genomic: CCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAG

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: 44 (upstream exon), 46 (downstream exon)
Score: 12

GCGGCGCATGCGGGTGGCCTTCACCTGCAACGTGTGCGGGCAGCGTACGACCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggacta ... actgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTTCATGAGATGAAGTGCTACGTCGGTCCAGACTTCCGCTACCAAGGGGATG

Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 21

Block sizes: 49 (upstream exon), 18 (downstream exon)
Score: 2

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 27

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctggtgcaaactgtttgctttcccacattttctgaatttttgtctactgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTTCATGAGATGAAGTGCTACGTCGGTCCAGACTTCCGCTACCAAGGGGATG

                          attttctgaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataagtcgttcttctccacatttggatgttgtcgttttcctttccctggtgcaaactgtttgctttcccacattttctgaatttttgtctactgttgcagTGCTGCGGTTGCAATGTGTTCCATAAGTTGGTCGACAACCTGAACCTGTTTCATGAGATGAAGTGCTACGTCGGTCCAGACTTCCGCTACCAAGGGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - -ctccaca
- - - - - - - - - - - - -atgttgt
- - - - - - - - - - - - - - - - - - - - - - -ctggtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - actgttt