ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGGCAGCGAGTGGGAAGGCATGTCGCTGGGGCAGATGATGCTCGCCTCCTTCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttggccatcgcctgctgcgcatctatgcttacttgcgtatgctgccagtagctaactcttggccatgttttcag

Basic information

species	Zea mays
transcript	GRMZM2G042080_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G042080_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g02500.1 (Oryza sativa), 5'ss of exon 3

TGGCAGCGAGTGGGAAGGCATGTCGCTGGGGCAGATGATGCTCGCCTCCTTCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttggccatcgcctgctgcgcatctatgcttacttgcgtatgctgccagtagctaactcttggccatgttttcag
|||||| |||||||| || |||||||||||||||||||||||  |||||||||||||||||||||||   |||||||| |||||||||||||| ||||||||| ||||  |                   |||||| |  ||  | | || |   |  |||| |  ||| |||  ||| ||
TGGCAGTGAGTGGGAGGGGATGTCGCTGGGGCAGATGATGCTATCCTCCTTCAATGAGGGCAGGGAGGCACCCCATCCCCCCTTCTTCCATGCTGCACAGgtatcattccg-------------------tatgctgagctgtatgtcctccatatgactaattactggacattcttttag

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|76932372|gb|DV173030.1|DV173030

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

EST: gi|76287059|gb|DV026627.1|DV026627

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

EST: gi|71421895|gb|DR805584.1|DR805584

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

EST: gi|148959395|gb|EC905430.2|EC905430

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

EST: gi|89252849|gb|DY624635.1|DY624635

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGCCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

EST: gi|33467070|gb|CF244119.1|CF244119

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

EST: gi|148935525|gb|EC879566.2|EC879566

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTC-ATGCCGCACAG                         GTATGGAACCATGATTTCTATTGCCGATCCATG
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATG

EST: gi|149075255|gb|EE163758.2|EE163758

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

EST: gi|148993468|gb|EE033787.2|EE033787

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

EST: gi|50329231|gb|CO524357.1|CO524357

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

EST: gi|5398723|gb|AI812188.1|AI812188

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCG
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCG

EST: gi|50331822|gb|CO526948.1|CO526948

EST:     TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAG                         GTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC
genomic: TCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGC

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: 34 (upstream exon), 47 (downstream exon)
Score: 11

TGGCAGCGAGTGGGAAGGCATGTCGCTGGGGCAGATGATGCTCGCCTCCTTCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttg ... atgttttcagGTATGGAACCATGATTTCTATTGGCGATCCATGAAACCTGGTGGCGGGGGCAAGCCACCGGAACGGCTCCTGAAGTTTATCAATAGAGACTTTGGCTCCC

Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 51

Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 13

Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 11

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCAGCGAGTGGGAAGGCATGTCGCTGGGGCAGATGATGCTCGCCTCCTTCAATGAGGGCAGGGAGCAGCCCCATCCTCCCTTCTTCCATGCCGCACAGgtaccatttggccatcgcctgctgcgcatctatgcttacttgcgtatgctgccagtagctaactcttggccatgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG