ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGGCATGAATGATAGAGGGGTCTCATATACCTTTGGTGCTGACAAGGTTTCAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattgcatgcgatgtgatgtcag

Basic information

species	Zea mays
transcript	GRMZM2G160237_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G160237_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g16110.1 (Oryza sativa), 5'ss of exon 2

GGGCATGAATGATAGAGGGGTCTCATATACCTTTGGTGCTGACAAGGTTTCAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattgcatgcgatgtgatgtcag
||||||||||||||| ||||||||||| || |||||||||||||| |||||||||||| || |||| ||||| ||||||||||| || || || || |||||||          |||| |||| | ||| ||    ||  | | |||    || |||||     |||   | |||||||| |||| ||||| |      
GGGCATGAATGATAGGGGGGTCTCATACACTTTTGGTGCTGACAAAGTTTCAGAATTCCTGGAAAAACATGACCTTGATCTTATTTGCCGGGCACATCAGgtacaat-------tttaatgcaacatcttttcctttcagtattttttttggtcaactgagg--tgatcatatttatatttcatgtgatgtcag-----

upper sequence: GRMZM2G160237_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT2G29400.1 (Arabidopsis thaliana), 5'ss of exon 2

GGGCATGAATGATAGAGGGGTCTCATATACCTTTGGTGCTGACAAGGTTTCAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattgcatgcgatgtgatgtcag
||||||||||||| | || || ||||| || ||||| |||||||| ||  |||| |||||| | || |||||  | || |||||||||||||| ||||||||      ||| | |    |  | || |  ||| | |  || |           |||   || ||||  || ||     ||  |               
GGGCATGAATGATCGTGGTGTTTCATACACTTTTGGAGCTGACAAAGTCGCAGAGTTCTTGGAGAAACATGACATGGACCTTATCTGTCGTGCCCACCAGgt-----tttaacttgagttatatctgccatttagtttattatgaaaactgtgcaaccttaatttgagtgtattggctctgtttatag-----------

upper sequence: GRMZM2G160237_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0019g02410.t01 (Vitis vinifera), 5'ss of exon 2

GGGCATGAATGATAGAGGGGTCTCATATACCTTTGGTGCTGACAAGGTTTCAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattgcatgcgatgtgatgtcag
||| |||||||| ||||| ||||||| |||||||||  |||| || || ||||||||||||  ||| |||||| | || ||| | |||||||| || |||||      || ||||||        || | | ||| ||| |||   |||       ||| ||| ||||  | ||  | | |  |               
GGGGATGAATGACAGAGGTGTCTCATTTACCTTTGGGCCTGATAAAGTGTCAGAATTCTTGACAAAACATGATTTAGACCTTGTTTGTCGTGCCCATCAGgt----tattggcattt----ttagttttctcttgttctattttactcat-----gctgaaaactgaaattcttcttttggtctag-------------

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|108823835|gb|EC277843.1|EC277843

EST:     CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAG                         GTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA
genomic: CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgcctt ... gtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA

EST: gi|76280337|gb|DV019905.1|DV019905

EST:     CAGAATTCTTGCAAAAGCATGATCTTGATTTTATCTGTCGTGCTCACCAG                         GTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA
genomic: CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgcctt ... gtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA

EST: gi|32934896|gb|CF039708.1|CF039708

EST:     CACAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAG                         GTTGTCGAGGATGGGCATGAATTTTTTGCTGACAGACAG
genomic: CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgcctt ... gtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAG

EST: gi|60395923|gb|DN228793.1|DN228793

EST:     CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAG                         GTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA
genomic: CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgcctt ... gtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA

EST: gi|78115397|gb|DV533785.1|DV533785

EST:     CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAG                         GTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA
genomic: CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgcctt ... gtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA

EST: gi|31362821|gb|CD447178.1|CD447178

EST:     CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTCTCGTGCTCACCAG                         GTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA
genomic: CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgcctt ... gtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA

EST: gi|31353876|gb|CD438233.1|CD438233

EST:     CAGAATTCTTGCACCCCCATGATCTTGATCTTATCTGTCGTGCTCACCAG                         GTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA
genomic: CAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgcctt ... gtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA

EST: gi|14243601|gb|BG841261.2|BG841261

EST:     CTTGATCTTATCTGTCGTGCTCACCAG                         GTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA
genomic: CTTGATCTTATCTGTCGTGCTCACCAGgtaccgcctt ... gtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATA

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: 322

GGGCATGAATGATAGAGGGGTCTCATATACCTTTGGTGCTGACAAGGTTTCAGAATTCTTGCAAAAGCATGATCTTGATCTTATCTGTCGTGCTCACCAGgtaccgcctt ... gtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATATTCTCGGCCCCCAATTATTGTGGTGAATTTGATAATGCTGGTGCAATGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 416