ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctatccag

Basic information

species	Zea mays
transcript	GRMZM2G075485_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G075485_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 5'ss of exon 5

AGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactg-gtccaacaggcttgttttaatttctatattggcattgttcccttctatccag
||||||| |||||||||||||||||||| || ||||||||||||||||| |||| |||||||||||| || || ||||||| ||| |||||||||||||||||  ||     || |||| | |           || | ||   | ||| | ||| ||  | || ||      |     | | ||  |||||||| ||    | || ||||| ||| |||
AGGCTGATATTGAAGAATTTGAAGCTAAGTACAGAGGGTCAGATTCTGAAAAAAAGGACTTGAAGGATCTATATACAAAATTTAAAGGCAACATGAACAGgtggcttac--aaaatttagtgt-----------tgattaattttctatacagaaggcaatgaattgcaagtgaataattgggttccatttctattttaatttggtgcccttgtatgcag

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|71757753|gb|DR955690.1|DR955690

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|91870824|gb|EB401103.1|EB401103

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|78074189|gb|DV502623.1|DV502623

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|32845400|gb|CD985081.1|CD985081

EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|78116316|gb|DV534703.1|DV534703

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTG
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTG

EST: gi|32850389|gb|CD990070.1|CD990070

EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|211431464|gb|FL284143.1|FL284143

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|32844155|gb|CD983836.1|CD983836

EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|211342376|gb|FL103369.1|FL103369

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTT-CTGCGCAATG
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATG

EST: gi|211339995|gb|FL103365.1|FL103365

EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCCACATGAACAG                         GCTTTTCTGCGCAATGATTTG
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTG

EST: gi|211339988|gb|FL103358.1|FL103358

EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAA
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAA

EST: gi|60341956|gb|DN208929.1|DN208929

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|78074190|gb|DV502624.1|DV502624

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|148958293|gb|EC904513.2|EC904513

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|32909541|gb|CF014353.1|CF014353

EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|148958294|gb|EC904514.2|EC904514

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|78117499|gb|DV535886.1|DV535886

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|32945462|gb|CF050281.1|CF050281

EST:     AAAACGGACTTGAAGGACCTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTAGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|32844895|gb|CD984576.1|CD984576

EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|211339992|gb|FL103362.1|FL103362

EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCAC
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCAC

EST: gi|60351082|gb|DN218055.1|DN218055

EST:     AGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|71772229|gb|DR970166.1|DR970166

EST:     AAAACGGACTTGAAGGAACTTTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

EST: gi|71435377|gb|DR816427.1|DR816427

EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT

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: 47 (upstream exon), 48 (downstream exon)
Score: 266

AGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 58

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 54

Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 76

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA