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

gtaatataatattaaataagttgaagctgctgcaagaataatttggcatcggtctatatatttttacctttgagctatcatggtttctttgtaaatgctaccggaatatatggtgcttccacctgttgtgacatgtttctctgtttgtttgtttcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGA

Basic information

species	Zea mays
transcript	GRMZM2G103812_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 4

gtaatataatattaaataagttgaagctgctgcaagaataatttggcatcggtctatatatttttacctttgagctatcatggtttctttgtaaatgctacc-ggaatatatggtgcttccacctgttgtgacatgtttctctgtttgtttgtttcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGA
                                                                                 |  |    |||  |  |||   || ||  ||   ||   || |   |   | |    | | |   || || | | |  |||||||||||||||||||||||||||||||||| ||||| ||||| ||||||||| | |||||||||||||| |||||||||||||| || |||||||| ||||
-----------------------------------------------------------------------------gtgcgtatcaaatgttgagactaaaagggatgcatcaagccgtcaacatatcaaataaccatatatcactgcttttcttctgtgcagGTGAGGTTTTTACATGATCCATCAAAGGATACTGGGTATGTGGGCTGTGCTCTGACAAGCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGA

upper sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 4

gtaatataatattaaataagttgaagctgctgcaagaataatttggcatcggtctatatatttttacctttgagctatcatggtttctttgtaaatgctaccg-gaatatatggtgcttccacctgttgtg-acatgtttctctgtttgtttgtttcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGA
            | | |      ||  |  | ||  | |  ||||   |  |  ||   | |   |  |   |  | |  |  | |  || |  ||| ||    ||  |||||      |    |  | |  |||||| | ||| |   | | | |  | ||||| | || ||  | |||||||| || || || || || | ||| || ||||| |||||||||||||||||| |||||||||||||| | ||||| || ||||
-----------gtgagttttggaaatataatccaccattgctttgctttttggttaagaaatagcaaatgctacatttttttctctaattttgcatgttattatgaccatatgtgttaacggtttactatctacatgtgtatct-tcaatctttcttgcttgcagATAAGATTCCTGCATGATCCTTCTAAAGATACAGGGTTTGTAGGTTGTGCCTTAACAAGCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGA

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|6021033|gb|AW065961.1|AW065961

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|5895606|gb|AW036852.1|AW036852

EST:     TGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGTTGTGCT
genomic: TGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|149083207|gb|EE172484.2|EE172484

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGC
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGC

EST: gi|85151683|gb|DW587480.1|DW587480

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGTTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|38502601|gb|CF972461.1|CF972461

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGTTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|5268463|gb|AI770427.1|AI770427

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|31355194|gb|CD439551.1|CD439551

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|31354133|gb|CD438490.1|CD438490

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|60355186|gb|DN222159.1|DN222159

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|32941574|gb|CF046393.1|CF046393

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGTTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|31349415|gb|CD433772.1|CD433772

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|31360531|gb|CD444888.1|CD444888

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|6994143|gb|AW453357.1|AW453357

EST:     GATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: GATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|67021527|gb|CO450276.1|CO450276

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|31355476|gb|CD439833.1|CD439833

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|31356060|gb|CD440417.1|CD440417

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|40334707|gb|CK368777.1|CK368777

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGTTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|14701287|gb|BI233705.1|BI233705

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGTTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

EST: gi|67031397|gb|CO460146.1|CO460146

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGGTGTGCN
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGC-

EST: gi|32865912|gb|CF005594.1|CF005594

EST:     AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAG                         GTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGTTGTGCT
genomic: AGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCT

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), 49 (downstream exon)
Score: 375

GGATGGCCTGTATGGAAGGCACCTGCATGTGTACGACTGGCCTGGCGGTGAGCTCAAGCAGACACTTGATCTAGGTGACACTGGACTCCTTCCCCTTGAGgtaatataat ... tcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2018

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 973

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 620

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatggtgcttccacctgttgtgacatgtttctctgtttgtttgtttcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGA

                           tttctctgtttgtttg  CT-rich tract
                                   tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatataatattaaataagttgaagctgctgcaagaataatttggcatcggtctatatatttttacctttgagctatcatggtttctttgtaaatgctaccggaatatatggtgcttccacctgttgtgacatgtttctctgtttgtttgtttcccctgcagGTGAGGTTTTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA