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

gtaggttcccagtaaattaacatgtttgcggtttcaagttgatggtatacaagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC

Basic information

species	Zea mays
transcript	GRMZM2G130034_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 6

-gtaggttcccagtaaattaacatgtttgcggtttcaagttgatggtatac--aagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC
  | | ||   ||| |||||| | ||||  ||      |||  |  |||||  | || |  |||||||| |||||||   |||||| |||| ||||| |||||||||||||||||| |||||||||| |||||||||||||| || ||||||||||||||||| ||||||||
gttggattgtgagttaattaataagtttatggaaaattgttcttcttatactcatgtgtgttcttacaacagGTATCAAAATTGGCGTTGTCACTGCTATTGCTGCTCCTGCAAGTATTAAGGTGGAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGC

upper sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 6

------------------gtaggttcccagtaaattaacatgtttgcggtttcaagttgatggtatacaagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC
                   |  |     |  || ||    | ||| |  | |    ||   | ||   |  || | | | || | |||| |   ||| ||  |||| || || ||||||||||| |||||| | |||||||| |||||||| ||||| ||||||||||| || || || |||||   
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagttaataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA

upper sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 6

----------gtaggttcccagtaaattaa---catgtttgcgg-tttcaagttgatggtatacaagtct-tctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC
           |  |||| || |  |||     ||      |   ||||||  |     | ||   |||| | | ||    |||| ||  ||||||||||||| ||||| |||||||| ||||||||| | || ||||| |||||||| ||||| || ||||| || || ||  |||||||   
gtaggcctctttctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtctatattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA

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|148941174|gb|EC886056.2|EC886056

EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGG                         GTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGG
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGG

EST: gi|31359313|gb|CD443670.1|CD443670

EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGG                         GTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGG
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGG

EST: gi|148983478|gb|EE029496.2|EE029496

EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAA-GGAGG                         GTATCCCTATTGGCAT
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCAT

EST: gi|149103753|gb|EE289159.2|EE289159

EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGG                         GTATCCCTATTGGCATTGTTACTGCAATTGC
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGC

EST: gi|148940595|gb|EC885401.2|EC885401

EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGG                         GTATCCCTATTGGCATTGTTACTGGCA-TTGCTGCTCCTGCAAGTCTTAAG
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCATTGTTACTG-CAATTGCTGCTCCTGCAAGTCTTAAG

EST: gi|148944452|gb|EC889567.2|EC889567

EST:     GCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTTAGAAAAG-AGG                         GGATCCCTATTGGC
genomic: GCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTT-AGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGC

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: 74

TTGAATCTAGAGGACCTGCATAGCGTATTTTTAAAGACAGACAAATACTCTGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 48

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 47

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 30

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aattaacatgtttgcggtttcaagttgatggtatacaagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC

                                       tcttctcttac  CT-rich tract
                                              ttacaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttcccagtaaattaacatgtttgcggtttcaagttgatggtatacaagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT