ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...tccctttcttagactccactcatgtgggagcctccgacactggatctgcccattgtttcactattgcaatgccatttaagtttgctgatattcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT

Basic information

species	Zea mays
transcript	GRMZM5G868588_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G868588_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g33450.2 (Oryza sativa), 3'ss of exon 2

--------tccctttcttagactccactcatgtgggagcctccgacactggatctgcccattgtttcac-tattgcaat-gccatttaagtttgctgatattcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT
        |   |||  || | || ||| || |       |  |  | |   ||| |   | |||||||  |||| | |      | |   ||   ||| || ||||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||||||| ||||||||||||||||| ||| |  | |||||||||||||
gctgaccgttttttttataaattc-acttatata------tttgcaattatttcttc---tagtttcacgcattggattcattgataacaattatggatctttttttcagGAGTTTTTCTTGCAAGGCCGGTTCATTTTTGGACCAGATGTGAGATCTTTGTTTCTCACTATATTCCTCATTCTTGCACCAGTATTAGTCTTCTGTATAT

upper sequence: GRMZM5G868588_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 1

tccctttcttagactccactcatgtgggagcctccgacactggatctgcccattgtttcactattgcaatgcc-atttaagtttgctgatattctttt-cagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT
                                      || |  |||  ||||| | | |||||     |||  ||| |    |  |   ||| | || ||| | |||||  | |||||  |||||||||||||||| |||||||||||| ||   || || ||  | || ||| |||| ||  | |  || |||||| | |
------------------------------------gtacagtttctatccatt-tatgactatgagggtgcttattcattgcttttatcattttcttgcagAAATTTTTTCTTCAAGGAAGGTTCATATTTGGACCAGATGTGAGATCACTGGCGCTGACAATTATTCTTATTGTTGCTCCTGTTGCAGTTTTCTGTGTCT

upper sequence: GRMZM5G868588_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G05670.1 (Glycine max), 3'ss of exon 1

-tccctttcttagactccactcatgtgggagcctccgacactggatctgcccattgtttcactattgcaatgccatttaagtttgctgatattctttt--cagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT
   |   | ||| | | || |  | |  ||   |  |  || |  |||  ||||| | | |||||     |||   || | |    ||||| | || |  ||| | |||||  | |||||  |||||||||||||||| |||||||||||| ||   || || ||  | || ||  |||| ||  | |  || |||||| | |
agacaaatgtta-attgcattgttatttgaaa-tatgttacagtttctatccatt-tatgactatgagggtgcttattcattgctttgataattttcttgcagAAATTTTTTCTTCAAGGGAGGTTCATATTTGGACCAGATGTGAGATCACTGGCACTGACAATTATTCTTATCGTTGCTCCTGTCGCAGTTTTCTGTGTCT

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|211226409|gb|FL202758.1|FL202758

EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

EST: gi|211226410|gb|FL202759.1|FL202759

EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

EST: gi|211226406|gb|FL202755.1|FL202755

EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGNCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

EST: gi|211226399|gb|FL202748.1|FL202748

EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

EST: gi|94479844|gb|EB708802.1|EB708802

EST:     CACTGCCGGAGAGCAGCCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCCAGGGCGGTTCATATTTTGGACCCGATGTGAGATCATT
genomic: CACTGCCGGAGAGCAGCC-TAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTT-GGACCTGATGTGAGATCATT

EST: gi|211226404|gb|FL202753.1|FL202753

EST:     TCACTGCCGGAGAGCAGCCTAGGGTTTACMAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

EST: gi|211226401|gb|FL202750.1|FL202750

EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

EST: gi|211226408|gb|FL202757.1|FL202757

EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGGTCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

EST: gi|148970678|gb|EE021391.2|EE021391

EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

EST: gi|211226405|gb|FL202754.1|FL202754

EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGAAAGCAAC                         GNAGTTTTTCTTTTGCA-GGCCGNTTCATATTTGGGACCTGATGGTGAGAT
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagG-AGTTTTTCTT--GCAAGGCCGGTTCATATTTGG-ACCTGATG-TGAGAT

EST: gi|88747254|gb|DY531395.1|DY531395

EST:     GCACTGCCGGAGAGCACCCTAGGGTTTACCAAGTTTGGAGAGGAAGCAAC                         GAGTTTTTCTTGCAGGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

EST: gi|76013624|gb|DT940794.1|DT940794

EST:     GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAAC                         GAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG
genomic: GCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTG

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), 49 (downstream exon)
Score: 167

GAGGGAGCTAGAGATGTACGGACCGCCGTCCCGAGGCGGCGGGGGAGCTGGCACTGCCGGAGAGCAGCCTAGGGTTTACCAAGTTTGGCGAGGAAGCAACgtgagctctc ... ttcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 181

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgcccattgtttcactattgcaatgccatttaagtttgctgatattcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT

                                     tgctgat  putative branch site (score: 181)
                                           tattcttttc  CT-rich tract
                            atttaagttt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccctttcttagactccactcatgtgggagcctccgacactggatctgcccattgtttcactattgcaatgccatttaagtttgctgatattcttttcagGAGTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCATTGTTTCTCACCATATTCCTCATTCTTGCGCCAATGGTGGTCTTCTGTATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - catgtgg
- - - - - - - - - - - - - - - - - - -cactgga
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat