ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TACTAGCGTTGCATCCTTCTTTGTCAGCCGAGTGGACACCCTTATTGACAAAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaactataattaactgcctcttgatgttagaaacttttaaactgtccacaaagttatgcaatatgaccatactctatcatgtcag

Basic information

species	Zea mays
transcript	GRMZM2G134256_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G134256_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g70170.1 (Oryza sativa), 5'ss of exon 4

TACTAGCGTTGCATCCTTCTTTGTCAGCCGAGTGGACACCCTTATTGACAAAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaactataattaactgcctcttga-------tgttagaaacttttaaactgtccacaaagttatgcaatatgaccatactctatcatgtcag
 || || || || |||||||||||||||||||| ||||| ||||||||||||||||| || ||||| |||||||||||||| |||||| | ||||||||||||  || ||  | |||||  |||||| | |         |||| || ||  |||||  |        | |||| | ||  ||  || ||| |      
GACCAGTGTAGCGTCCTTCTTTGTCAGCCGAGTTGACACACTTATTGACAAAATGCTCGAGAAGATCGGAACACCTGAGGCACTTGCCCTCAGAGGAAAGgtacgcacaatcaaaattacatgcctcctaagtcctagcattaggaatttccaaactagcagttctaatctgcattttggtcactctgtattacag---

upper sequence: GRMZM2G134256_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 5'ss of exon 5

TACTAGCGTTGCATCCTTCTTTGTCAGCCGAGTGGACACCCTTATTGACAAAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaa---acaaaactataattaactgcctcttgatgttagaaacttttaaact--gtccacaaagttatgcaatatgaccatactctatcatgtcag
||| || ||||| |||||||||||||| || || |||||||| ||||||||  ||||||| || |||||||| || ||||||||||   |  ||||||||||||   |  ||  || ||| || |     |     || ||   ||| |||||  |  |  ||  | |||  |  |    ||  ||||         
TACAAGTGTTGCCTCCTTCTTTGTCAGTCGGGTAGACACCCTCATTGACAAGTTGCTTGAGAAAATTGGAACTCCAGAGGCCCTTGATCTCCGAGGAAAGgtaataaattaatttacaatcaaattgtcatc--cttttgagggtttaaaactcaggacctaatatcatgggacttttatatgttctag--------

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|148933154|gb|EC876793.2|EC876793

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTTTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|40335818|gb|CK369888.1|CK369888

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|60357531|gb|DN224504.1|DN224504

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|67033538|gb|CO462287.1|CO462287

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|32850249|gb|CD989930.1|CD989930

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|32907897|gb|CF012710.1|CF012710

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|6626605|gb|AW258137.1|AW258137

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|32850213|gb|CD989894.1|CD989894

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|5928815|gb|AW056107.1|AW056107

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|32850218|gb|CD989899.1|CD989899

EST:     AATGCTTGACAAGATT-GAACCACTTGAGGCCC-TGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAAAAGAAATTC
genomic: AATGCTTGACAAGATTGGAA-CACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|37387548|gb|CF630971.1|CF630971

EST:     TGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: TGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|166532676|gb|EG182361.1|EG182361

EST:     ATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: ATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|32943331|gb|CF048150.1|CF048150

EST:     GCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: GCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|60354154|gb|DN221127.1|DN221127

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|60357634|gb|DN224607.1|DN224607

EST:     TTGAGAGG-AAG                         GCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: TTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|21432436|gb|BQ547926.1|BQ547926

EST:     GAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: GAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|60400687|gb|DN233494.1|DN233494

EST:     GAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: GAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|211497584|gb|FL092454.1|FL092454

EST:     AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: AAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

EST: gi|37383227|gb|CF628606.1|CF628606

EST:     TGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAG                         GCTGCAGTAGCGCAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC
genomic: TGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTC

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: 255

TACTAGCGTTGCATCCTTCTTTGTCAGCCGAGTGGACACCCTTATTGACAAAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaa ... atcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTCTCTGGCCCAAGGTGGGAGGCGTTGGCCAAGAAAGGTGCCAAGAAACAAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 882

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 900

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 577

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTAGCGTTGCATCCTTCTTTGTCAGCCGAGTGGACACCCTTATTGACAAAATGCTTGACAAGATTGGAACACCTGAGGCCCTTGCCTTGAGAGGAAAGgtaaacaaaactataattaactgcctcttgatgttagaaacttttaaactgtccacaaagttatgcaatatgaccatactctatcatgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA