ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTCGACAGTTTCTTGGGGCAGCGACGGACAACTGACCATGAAGCCATGACTAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctcttatactttgccttctgctctgtattcaacattgaatattcatttgttgctaacgattaacggtaatgctcatgagcgcgcaagtggcat...

Basic information

species	Zea mays
transcript	GRMZM2G158136_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158136_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g50050.2 (Oryza sativa), 5'ss of exon 3

GTCGACAGTTTCTTGGGGCAGCGACGGACAACTGACCATGAAGCCATGACTAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctcttatactttgccttctgctc-tgtattca-acattgaatattcat-ttgttgctaacgat-taacggta--atgctcatgagcgcgcaagtggcat
||||| ||||||||||| |||||||||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||||||||| || ||| ||| |    | ||| ||| |    ||  |  ||  | | |||  || | ||  ||| |  |||| ||  ||   |   || ||| | |    | || ||  | 
GTCGATAGTTTCTTGGGCCAGCGACGGACAACGGACCACGAAGCTATGACTAATATGAAGACTGAGTTCATGTCCCTCTGGGATGGCTTCACCACTGATCgtaagtac----acactctgcttcaaacttatacatgaacatattccatgtccaaattgctagtaactatgcaaatatcctattctctttattatgtaa-tgata-

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|67030530|gb|CO459279.1|CO459279

EST:     AATATGAAGACAGAAGT-CATGTCCCTCTGGGATGGCTTCAC-ACCGACC                         AGAATGCTCGTGTAATGGTCCTGGCTGCTANCAA-CAGGCCTTCTGAGCTA
genomic: AATATGAAGACAGA-GTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTA-CAAACAGGCCTTCTGAGCTA

EST: gi|148961917|gb|EE012707.2|EE012707

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCAC-ACCGACC                         AGAACGCTCGTGTAA
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAA

EST: gi|78081860|gb|DV510272.1|DV510272

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|211461323|gb|FL283286.1|FL283286

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAATGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|148949884|gb|EC895380.2|EC895380

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|74244276|gb|DT652190.1|DT652190

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|78121665|gb|DV540049.1|DV540049

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|93283899|gb|EB676163.1|EB676163

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|148954924|gb|EC900412.2|EC900412

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAA
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAA

EST: gi|149077190|gb|EE165854.2|EE165854

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|76923334|gb|DV169435.1|DV169435

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|78075677|gb|DV504111.1|DV504111

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|71299644|gb|DR785830.1|DR785830

EST:     GAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: GAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|149089069|gb|EE178236.2|EE178236

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGNTA-TGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTA
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTG-TAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTA

EST: gi|31354032|gb|CD438389.1|CD438389

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACTGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAG

EST: gi|71299646|gb|DR785831.1|DR785831

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|148941166|gb|EC886045.2|EC886045

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGG

EST: gi|148961232|gb|EE011948.2|EE011948

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|93012345|gb|EB637865.1|EB637865

EST:     AATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCCTCCCCCACCGACC                         AGAACGCTCGTGTAATGGTCCTG
genomic: AATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACC-ACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTG

EST: gi|148940585|gb|EC885389.2|EC885389

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|148960540|gb|EE011147.2|EE011147

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCCCCACCGACC                         AGAACGCTCGTGTAA
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAA

EST: gi|149017489|gb|EE045689.2|EE045689

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAA
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAA

EST: gi|148944282|gb|EC889378.2|EC889378

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

EST: gi|91053937|gb|EB164355.1|EB164355

EST:     TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACC                         AGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG
genomic: TAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAG

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: 45 (upstream exon), 49 (downstream exon)
Score: 64

GTCGACAGTTTCTTGGGGCAGCGACGGACAACTGACCATGAAGCCATGACTAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctc ... ctcttttcagAGAACGCTCGTGTAATGGTCCTGGCTGCTACAAACAGGCCTTCTGAGCTAGATGAGGCCATCCTTAGGCGCTTTACTCAGATATTTGAAATTGGAATTCC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 83

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGACAGTTTCTTGGGGCAGCGACGGACAACTGACCATGAAGCCATGACTAATATGAAGACAGAGTTCATGTCCCTCTGGGATGGCTTCACCACCGACCgtgagtcctcttatactttgccttctgctctgtattcaacattgaatattcatttgttgctaacgattaacggtaatgctcatgagcgcgcaagtggcat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA