ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtactgtggttttaatctgtggaaatcatctatgttttttctgaatataccttatctggaaatcatctattgaaacagtttggagtaggagttgctttta...

Basic information

species	Zea mays
transcript	GRMZM2G376731_T01
intron #	18
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os04g59494.4 (Oryza sativa), 5'ss of exon 18

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtact-gtggttttaatctgtggaaatcatctat-gttttttctgaatataccttatctggaaatcatctattgaaacagtttggagtaggagttgctttta
||||||||||||||| ||  | ||||| || |||||||||||| |||| ||||| |||||| |||| ||||| || ||||||||||||||||| || ||||||||    |||||  ||||||   | | ||| | ||||   |    || |  | || || |  ||   |  | |  || ||| ||| |    ||||  |  
AGATATATTTATGCCACCACTAATCACAAAATGGCAGCAACTTGCCAACTCTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAGgtacttacagtttttgtctgtgcttaccttctctagtttgaacatgctaaatttgatttgaaggtcccttcat-acccattttagagcatcttttgcgata-

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA10G42960.1 (Glycine max), 5'ss of exon 18

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtactgtggttttaatctgtggaaatcatctatgttttt-tctgaatataccttatctggaaatcatctattgaaac--agtttggagtaggagttgctttta-------------------------------------------------
 || ||  | ||||| || || ||   ||| |||||||||||||| ||||| ||||||||||| ||||||||||| |||||||||||||||||  |||| ||| ||    | |  | |    | ||  |  ||| |  | | ||  |  |  ||   ||| ||  ||||||  ||    |  ||   ||| |   ||    |                                                  
TGACATTCTCATGCCACCATTAATTGAGAAATGGCAGCAACTTTCAAATTCAGACAAAGATCTTTTTCCACTCCTGGAATGCTTTACATCTATATCACATgta-tgcacatctgtttttccaacatattacatgataatatatgggtggaatttg--tgggaacgatctatataatttgaaatttttgtatggactgtaactgtatcatcatatctattttcttgtttctgatggtgttccattttatacag

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA20G24040.1 (Glycine max), 5'ss of exon 18

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtactgtggttttaatctgtggaaatcatctatgttttt-tctgaatataccttatctggaaatcatctattgaaac--agtttggagtaggagttgctttta------------------------------------------------
 || ||  | ||||| || || ||   |||||||||||||||||| ||||| ||||||||||| ||||| ||||| ||||||||||||||||| ||||| |||| |   | |   | |     |  | | ||||||  | | || ||  |  ||    || ||| ||||||  ||    |  ||   ||| |   ||    |                                                 
TGACATTCTCATGCCACCATTAATTGAGAAGTGGCAGCAACTTTCAAATTCAGACAAAGATCTTTTTCCGCTCCTGGAATGCTTTACATCTATAGCACATgtacggatatctgtttttccaacagac-tatatgttaatatatgcatggaatttggg-ggcaatgatctatataatttgaaatttttgtatggactgtaactgtacatcatatctattttcttgctcctgatggtgttccatttgatacag

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 18
lower sequence: AT2G16950.1 (Arabidopsis thaliana), 5'ss of exon 18

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtactg--tggtt-ttaatctgtggaaatcatctatgttttttctgaatataccttatctg--gaaatcatc--tattgaaacagtttggagtaggagttgctttta
 || ||  | ||||| ||  || |  | |||||||| |||||||| ||||| || ||||||||||||||| | || || ||||||||||| ||| | ||||||  |  |  || | ||  | |  | |  ||||||    |  ||  ||| |  | | |    ||||  |||  || |||  |   |  | | |    | |      
TGAGATTCTGATGCCTCCACTGGTTGCAAAGTGGCAACAACTTTCAAATTCAGATAAAGATCTATTTCCATTGCTAGAGTGCTTTACATCCATTTCTCAGgtatgggctacttgtcaaggtcttaagaatatctataaggt--cttgatacagttgaacgaatgaaactatccttaatgatcctactctgtgaaattatagt-----

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 18
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 5'ss of exon 18

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgta--ctgtggttttaatctgtggaa----atcatctatgttttttctgaatataccttatctggaaatcatctattgaaacagtttggagtaggagttgctttta
 |||||  | ||||| || || ||  | |||||||||| | |||||||||| |||||||| || |||||||| || || |||||||||||||| |||||||||  ||||  ||||  |   | | |    ||  |   |  | ||  | || | ||  |||      ||    ||||  |    ||      ||||          
TGATATTCTGATGCCTCCATTAATTGCAAAGTGGCAGCTAGTTTCCAATTCAGACAAAGACCTCTTTCCACTGCTAGAGTGCTTTACATCTATAGCACAGgtatgctgtactttttgttaataggacagtattgtacttagtcttgtttaacacactatataatctgatatgatattatattctttcaattgaggaaaaa------

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 18
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 5'ss of exon 18

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtact----gtggttttaatctg--tggaaatcat-ctatgttttttctgaatataccttatctggaaatcatctattgaaacagtttggagtaggagttgctttta
 |||||  | |||||||| |||||| | ||||||||||||||||| ||||| || |||||  | || ||||| || || |||||||||||||| ||||||||| |       || ||  | ||     ||   ||  ||| | |||  | ||   || || |||  | |  || ||   ||   || |    |     |  |     
TGATATTCTAATGCCGCCATTGATCGCAAAGTGGCAGCAACTTTCTAATTCAGATAAAGACATTTTCCCACTGCTGGAGTGCTTTACATCTATAGCACAGgtatttacgacagtcttcttttgaccttaagctatgttatttgtttgttcaaggaactttgtctacataatatata---aattggtatactatgatcatgcca----

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 18
lower sequence: EFJ11805 (Selaginella moellendorffii), 5'ss of exon 16

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtactgtggttttaatctgtggaaatcatctatgttttttctgaatataccttatctggaaatcatctattgaaacagtttggagtaggagttgctttta
  ||||| | ||||| || |||||  | || ||||| || ||  || |   ||||||||||||||||||||| || ||||| ||||| || || |||||||||     |||||  ||| |||  ||| ||  | ||    || |||     | |  | ||  |                                     
CAATATACTGATGCCACCATTGATAGCAAAATGGCAACAGCTCGCCGACAATGACAAAGATCTATTTCCACTTCTAGAATGTTTTACGTCCATCGCACAGgtat----gtttttttctttggttatcgtcgttattggc-ctaaat---tttcacattgacgtag-----------------------------------

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 18
lower sequence: EFJ22655 (Selaginella moellendorffii), 5'ss of exon 16

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtactgtggttttaatctgtggaaatcatctatgttttttctgaatataccttatctggaaatcatctattgaaacagtttggagtaggagttgctttta
  ||||| | ||||| || |||||  | || ||||| || ||  || ||  ||||||||||||||||||||| || ||||| ||||| || || |||||||||     |||||  ||| |||  ||| ||  | ||       | | |  | |   || |                                        
CAATATACTGATGCCACCATTGATAGCAAAATGGCAACAGCTCGCCGATAATGACAAAGATCTATTTCCACTTCTAGAATGTTTTACGTCCATCGCACAGgtat----gtttttttctttggttatcgtcgttattggcctaaattttcacattgatgtag---------------------------------------

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|91872776|gb|EB402733.1|EB402733

EST:     CTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAG                         GCATTGGGACCAGGATTTGCTCAGTTTGCGGAACCAGTGTTTCAAAGGTGC
genomic: CTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtactgtggt ... taatcttcagGCATTGGGACCAGGATTTGCTCAGTTTGCGGAACCAGTGTTTCAAAGGTGC

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), 47 (downstream exon)
Score: 209

AGATATATTTATGCCGCCTTTGATCACGAAGTGGCAGCAACTTTCCAATTCTGACAAAGATCTATTTCCACTCCTTGAATGCTTTACATCTATTGCACAGgtactgtggt ... taatcttcagGCATTGGGACCAGGATTTGCTCAGTTTGCGGAACCAGTGTTTCAAAGGTGCATCAATCTTATCCAATCGCAACAGTTGGCAAAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114