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

gtttgtacatgccctgctctagtcctgagcccatatgacatcttcatatactaactgatgctgaatgctactaccatcatggacatccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCAAGAAAATTCGTGAAGCCAGGGGTTACTCTTACATGGTTTG

Basic information

species	Zea mays
transcript	GRMZM2G165998_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G165998_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g06620.1 (Oryza sativa), 3'ss of exon 2

---------------gtttgtac---atgccctgctctagtcctgagcccatatgacatct----tcatat-actaactga--tgctgaatgctactac----catcatggacat-ccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCAAGAAAATTCGTGAAGCCAGGGGTTACTCTTACATGGTTTG
               | |   ||   |||    ||| | ||    | | | ||  | | ||     || ||  | ||   |  |||   ||| || |      ||  || || |  |||||  |||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||     
gtttgtgcatctattgctcaaacaatatgtttagcttttgtaactaactcttagtagaactagtgccaaattgccaaaaaacttgccagatgttaatgtggtgcacaattgatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG-----

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|50326887|gb|CO522013.1|CO522013

EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG                         AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGgtttgtacat ... ggacatccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG

EST: gi|211137227|gb|FL235054.1|FL235054

EST:     TCCTCATCATCGCGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG                         AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGgtttgtacat ... ggacatccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG

EST: gi|76289131|gb|DV028699.1|DV028699

EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG                         AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGgtttgtacat ... ggacatccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG

EST: gi|211137222|gb|FL235049.1|FL235049

EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG                         AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGgtttgtacat ... ggacatccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG

EST: gi|32864327|gb|CF004009.1|CF004009

EST:     TCCTCATCATCGCGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG                         AACTAGGAATATTAA
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGgtttgtacat ... ggacatccagAACTAGGAATATTAA

EST: gi|91869853|gb|EB400574.1|EB400574

EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCG                         AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGgtttgtacat ... ggacatccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATG

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: 926

GAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGgtttgtacat ... ggacatccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCAAGAAAATTCGTGAAGCCAGGGGTTACTCTTACATGGTTTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3474

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3778

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3258

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgacatcttcatatactaactgatgctgaatgctactaccatcatggacatccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCAAGAAAATTCGTGAAGCCAGGGGTTACTCTTACATGGTTTG

          atatactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtacatgccctgctctagtcctgagcccatatgacatcttcatatactaactgatgctgaatgctactaccatcatggacatccagAACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCAAGAAAATTCGTGAAGCCAGGGGTTACTCTTACATGGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC