ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TACAGCGGGCACGGCATACGGCTGCCCGCCGAGACCGGGAAGGACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgagatgtgcccctctgttgctaagttgctatgaaaatagggatcgaactgtaggtggaattattgaagtgtataagtggattgcatatcttctt...

Basic information

species	Zea mays
transcript	GRMZM2G066041_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G066041_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g41670.1 (Oryza sativa), 5'ss of exon 1

TACAGCGGGCACGGCATACGGCTGCCCGCCGAGACCGGGAAGGACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgagatgtgcccctctgttgctaagttgctatgaaaatagggatcgaactgtaggtggaattattgaagtgtataagtgg-attgcatatcttctt
|||||||| ||||| |  |||||||| || ||||||||  ||||||||||||||||||||||||||||||||||||||| |||||||||||| ||||||||||   |    | || |  ||||    |  ||  |         |     ||| ||  | | ||||    ||  | |   || |   |||      |  | 
TACAGCGGCCACGGGACGCGGCTGCCGGCGGAGACCGGCCAGGACGACGACACCGGCTACGACGAGTGCATCGTGCCCTCCGACATGAACCTCATCACAGgtgattgctccgcgcgctgctgtctacattttttttgtcgtcctgcttcggaattggggatcgaataggcgagatttgagagggacgttgtccgattgtt-

upper sequence: GRMZM2G066041_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv19s0085g01030.t01 (Vitis vinifera), 5'ss of exon 1

TACAGCGGGCACGGCATACGGCTGCCCGCCGAGACCGGGAAGGACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgagatgtgcccctctgttgctaagttgctatgaaaatagggatcgaactgtaggtggaattattgaagtgtataagtg-gattgcatatcttctt
|||||||| |||||||  || || || |||||||||||  |||||||||||||||||||||||||||||||||| ||    |||||||| ||||| || |||       |      | ||| |   |   |  || | |    |  | |    ||     ||| |      ||||  || | || ||  |  | | |||  
TACAGCGGCCACGGCACTCGACTCCCTGCCGAGACCGGAGAGGACGACGACACCGGCTACGACGAGTGCATCGTCCCTACTGACATGAATCTTATTACCGgtcaaaatcacaaattcttctttcatt---tccctctcatctcatcgttttctctaattctggga--gccaaagta-atgactgtgacggtttgttttcag

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|50334065|gb|CO529191.1|CO529191

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|94479091|gb|EB708049.1|EB708049

EST:     ACCGGCTACGACGAGTGCATCCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCC
genomic: ACCGGCTACGACGAGTGCATC-GTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCC

EST: gi|78083698|gb|DV512091.1|DV512091

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|91053253|gb|EB163671.1|EB163671

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCT
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCT

EST: gi|76286263|gb|DV025831.1|DV025831

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|37417517|gb|CF646412.1|CF646412

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|91873287|gb|EB403244.1|EB403244

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|78081107|gb|DV509519.1|DV509519

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|33467204|gb|CF244253.1|CF244253

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|94477128|gb|EB706086.1|EB706086

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|76020615|gb|DT947785.1|DT947785

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|50329168|gb|CO524294.1|CO524294

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|78118034|gb|DV536421.1|DV536421

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|76290481|gb|DV030049.1|DV030049

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|91049473|gb|EB159891.1|EB159891

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|50339633|gb|CO534759.1|CO534759

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTA

EST: gi|149098190|gb|EE184153.2|EE184153

EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAG                         ACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTN
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTT-

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), 47 (downstream exon)
Score: 37

TACAGCGGGCACGGCATACGGCTGCCCGCCGAGACCGGGAAGGACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgaga ... tgcaccgcagACCAAGATTTCACGGAGCTTGCGCAAAAAGTCCCCAGTGGCTGTCTCTTTACCATAGTTTCTGATTCGTGCCACAGTGGAGGGCTACTTGACAAGACCAA

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 16

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 31

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 12

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAGCGGGCACGGCATACGGCTGCCCGCCGAGACCGGGAAGGACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTTATCACAGgtgtgcgagatgtgcccctctgttgctaagttgctatgaaaatagggatcgaactgtaggtggaattattgaagtgtataagtggattgcatatcttctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctctg
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