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

...aaaaatagtcactcttattatttgtttagctataaatttgtgttatagtgttttgactgtatagttttatgtatcaacttcaactttttttgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAGCCTGCTCCTCAAACAGCTGCCTATGGCGCTTATCCTCCAACATACTCTG

Basic information

species	Zea mays
transcript	GRMZM5G808775_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G808775_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g11200.1 (Oryza sativa), 3'ss of exon 12

aaaaatagtcactcttattatttgttta-gctataaatttgtgttatagtgttttgactgtatagtttt--atgt-atcaacttcaactttttttgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAGCCTGCTCCTCAAACAGCTGCCTATGGCGCTTATCCTCCAACATACTCTG
     |     || | ||   |   ||   ||||   | | ||||||||| |||    |   || || |  |||  ||  |||   |   | ||||||||| ||||  | |||||||| ||||||||||| |||||||||||||||||||| ||  ||||||||||| ||||||| || ||||| ||||||||||||||| | |
----gtctctgctgtaatctgtcacttgtactatctctctttgttatagtatttcttttaactatttgttgatgcgattgactcttaacctgtttgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCG

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|28910345|gb|CB331392.1|CB331392

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|71765796|gb|DR963733.1|DR963733

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAN                         GCTGCATATCCTGCA
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCA

EST: gi|31405539|gb|CD484271.1|CD484271

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|24769068|gb|CA404197.1|CA404197

EST:     ATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: ATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|60400693|gb|DN233500.1|DN233500

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|71765795|gb|DR963732.1|DR963732

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|78026641|gb|DV495028.1|DV495028

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|113702536|gb|EE680040.1|EE680040

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|5058597|gb|AI737073.1|AI737073

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|50334965|gb|CO530091.1|CO530091

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|31405540|gb|CD484272.1|CD484272

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

EST: gi|76291475|gb|DV031043.1|DV031043

EST:     CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAG                         GCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG
genomic: CGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAG

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: 461

GTCAGCCACAGGAACTGATCCAAATGCTTCCAATCCTCCTGTTTGGCCTGCGACTTCTGAAACATCTGGACATCAATGGGGAGCTTCTTATGCTCAGCAGgtcaaacatt ... tgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAGCCTGCTCCTCAAACAGCTGCCTATGGCGCTTATCCTCCAACATACTCTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 273

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tagtgttttgactgtatagttttatgtatcaacttcaactttttttgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAGCCTGCTCCTCAAACAGCTGCCTATGGCGCTTATCCTCCAACATACTCTG

     ttttgac  putative branch site (score: 273)
                                cttcaacttttttt  putative PPT
              tatagttttatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaatagtcactcttattatttgtttagctataaatttgtgttatagtgttttgactgtatagttttatgtatcaacttcaactttttttgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAGCCTGCTCCTCAAACAGCTGCCTATGGCGCTTATCCTCCAACATACTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
aaaaata
- - - - - - - - - - - - - - - - - - -ttgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtat