ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgcttactttccactttcgacaatcgtcatcttctttcccctttcaggctttcacctgtaagacaatagcccgcttgttacttttaggcagcc...

Basic information

species	Zea mays
transcript	GRMZM2G059282_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G059282_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 5'ss of exon 2

TCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgcttactttccactttcgacaatcgtcatcttctttcccctttcaggctttcacctgtaagacaatagcccgcttgttacttttaggcagcc------------
|||| ||||||||| ||||||||||  | ||||| ||||||  ||||  |||||||||||||||||||||||| ||||| ||||||||||| ||||||||||   |       |||||||| ||   ||   | |||| || |||     |||  |   ||||  |||  | |||  |   |  | ||| ||| ||||              
TCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTACTCCAGgtaaat-------ctttccaccttttccacatgacatcctcattcagtcctcacac---cacccctaatcccata--ctagtcctaactcttatgcagttggatctagtttg

upper sequence: GRMZM2G059282_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G59140.1 (Arabidopsis thaliana), 5'ss of exon 2

TCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgcttactttccactttcgacaatcgtcatcttctttcccctttcaggctttcacctgtaagacaatagcccgcttgttacttttaggcagcc------
|||| ||  ||    | ||||  ||    ||||| || ||   |||||  || || |||||||| |||||||| ||||| ||||| || || |||||||||||||  |   ||  |  | ||||  ||  || |  ||| | ||   || |    | |     ||||  |   |   | | | |||   || ||     |      
TCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattatctaact--cgcttttcacc-tcttgctctacattgatctctagaacatggcattgtagtagtct---ctgttagttttcttcagaatcgcatcgct

upper sequence: GRMZM2G059282_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0004g05560.t01 (Vitis vinifera), 5'ss of exon 2

TCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgcttactttccactttcgacaatcgtcatcttctttcccctttcaggctt--tcacctgtaagacaatagcccgcttgttacttttaggcagcc
|  | || | |   || || || |||   ||||| |||||   ||||| ||| || ||||||||||||||||||||||| ||||| || || |   | ||||||  ||  || |  | ||     |  | |    |   ||  |    | |  |  ||  | |  || | ||  | |   ||| | ||  |||   |     
TTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgatttttccaatgcaaaaatgttacttaggaaaatcggttttgtgttggttttagtaatttgcatgaagacaattcgcatttttttttggtggga--

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|211141709|gb|FL287346.1|FL287346

EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT

EST: gi|211468741|gb|FL385438.1|FL385438

EST:     TCCTCGAGAAGATCTGCCAGTATTTSSTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: TCCTCGAGAAGATCTGCCAGTATTTC-TATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT

EST: gi|13490768|gb|BG517532.1|BG517532

EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT

EST: gi|211141707|gb|FL287344.1|FL287344

EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT

EST: gi|211491482|gb|FL425975.1|FL425975

EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT

EST: gi|18163997|gb|BM333836.1|BM333836

EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT

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: 110

TCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCTTATGATGGCCGCAAACTATCTGGACACTTGATGAGGAGCCTGAGGG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 371

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 272