ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatacttttggttgactttttatgacgtgttgctcctgcattatag

Basic information

species	Zea mays
transcript	GRMZM2G402242_T03
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G402242_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 5'ss of exon 5

GTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatacttttggttgactttttatgacgtgttgctcctgcattatag
||||||||||| | |||| ||| |||||||| ||||| |||||||| ||||||||||||||||| || ||  |||| ||  | ||||||||||||||| |||   || || |  |    |    |||        ||| ||| |     ||  || ||| ||| | | |  | | |              
GTGCTGCTCTCTTAAAAGTTGACAAGATTGTGACTGGACATAATGCTGATGACATTGCAGAAACTGTGTTATTGAATATATTACGTGGTGATATTGCACGgttagtgctgatcat----tcctttgtccttttttttctgtggttgatgttaaggctgattttcttt-atatatag--------------

upper sequence: GRMZM2G402242_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 5'ss of exon 6

GTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatacttttggttgactttttatgacgtgttgctcctgcattatag
||||||||||| | |||| ||| |||||||| ||||| |||||||| ||||||||||||||||| || ||  |||| ||  | ||||||||||||||| |||   || || |  |    | ||   |||     | |   || |  || |  || ||  |||| |||   |                   
GTGCTGCTCTCTTAAAAGTTGACAAGATTGTGACTGGACATAATGCTGATGACATTGCAGAAACTGTGTTATTGAATATATTACGTGGTGATATTGCACGgttagtgctgatcattcctt-tgtcctttttttgggtggttgatgttaatgctgattttctttatatatag-------------------

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|71774415|gb|DR972293.1|DR972293

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|91877954|gb|EB407911.1|EB407911

EST:     CTTGCGGAACATTCTGCGTGGGGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: CTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|71761950|gb|DR959887.1|DR959887

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTTTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|67014256|gb|CO443005.1|CO443005

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|50323940|gb|CO519066.1|CO519066

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|91872706|gb|EB402663.1|EB402663

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|60350684|gb|DN217657.1|DN217657

EST:     CCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: CCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|87157289|gb|DY402078.1|DY402078

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTG

EST: gi|91878573|gb|EB408530.1|EB408530

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGGGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGGGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|71770543|gb|DR968480.1|DR968480

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|91872707|gb|EB402664.1|EB402664

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

EST: gi|71770542|gb|DR968479.1|DR968479

EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG

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: 46 (upstream exon), 44 (downstream exon)
Score: 75

GTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTAT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 60

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 79