ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAGgtatgtttcttatcttgaataacttttagctgttgtttcatgaatttgcaacatcattgtatcagtataggagaacttcttagtcatcattgctgatttgttaatttctttttctaactcctttcataattcgtagacaatgttttaactaaaatcttcttttccttcgtcaaccag

Basic information

species	Zea mays
transcript	GRMZM2G170868_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G170868_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g37080.2 (Oryza sativa), 5'ss of exon 3

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAGgtatgtttcttatcttgaataacttttagctgttgtttcatgaatttgcaacatcattgtatcagtataggag--aacttcttagtcatcattgctga--tttgttaatttctttt--tctaactcctttca-taattcgta--gacaatgttttaactaaaatcttc--ttttccttcgtcaaccag
|||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||| ||||| |  ||||| ||| ||||||| |||||||||| | ||| || |||  ||    |  |   ||||||||| ||||| || |   |  ||   |   |  | |    |   | | ||| |  |   | |    ||  || ||| | ||     |  |  ||||| | |||  ||   ||| |    ||| | |  |||    |||| |||| | ||||||
TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTGTCAATGTCACATCATGTTGCAACTGTTGCGCTGATAGTTTTATCTTATGTGTTCAGgtctcttt-ttgtct--aacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaatattttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccag

upper sequence: GRMZM2G170868_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G12080.1 (Glycine max), 5'ss of exon 3

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAGgtatgtttcttatcttgaataacttttagctgttgtttcatgaatttgcaacatcattgtatcagtataggagaacttcttagtcatcattgctgatttgttaatttctttttctaactcctttcataattcgtagacaatgttttaactaaaatcttcttttccttcgtcaaccag
||||  | || ||||||||||| ||||| || || ||||||||||| |||   |||||||||||||||||  | || |||||||| |||||| | || |||||| ||| | ||      | ||||    | ||| | || ||   ||  | | |  ||||       |  ||    |  ||  |  | ||| |   | | | |||||  ||                                                                  
TTGCTTTAATATTTTGGGAAACGAGGCGCTCCGATTTTGGAGTGTCCATGAGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAGgtatctttttcat------tcactt----ccgttttgtcttgtcattcaagcttttttgtcctcaagttcgaccgttgattt-tgtttatttcatttgtctgaatttactt------------------------------------------------------------------

upper sequence: GRMZM2G170868_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G36370.1 (Glycine max), 5'ss of exon 3

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAGgtatgtttcttatcttgaataact-tttagctgttgtttcatgaatttgcaacatca--ttgtatcagtataggagaacttcttagtcatcattgctgatttgttaatttctttttctaactcctttcataattcgtagacaatgttttaactaaaatcttcttttccttcgtcaaccag
||||  | || ||||||||||| ||||| || |||||||||||||| |||   |||||||||||||||||  | || |||||||| |||||| | ||||||||||||| ||   |    | | | |||  ||  |  |||| |  |||    | |||  ||  |||||| | | |||  || ||  |  |||||  |  | ||                                                                             
TTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTGTCCATGAGTCATCATGTTGCTACTGTAATTCTCATTGTTCTGTCTTACATTTTCAGgtatgttttttcattcacttgagtgtttctcttgtcattcaagcttttttgtcctcaagtttgatcagttttgtagattttatttatt-tcatt--ttgtctg-----------------------------------------------------------------------------

upper sequence: GRMZM2G170868_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 3

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAGgtatgtttcttatcttgaataacttttagctgttgtttcatgaatttgcaacatcattgt-atcagtataggagaacttcttagtcatcattgctgatttgttaatttctttttctaactcctttcataattcgtagacaatgttttaactaaaatcttcttttccttcgtcaaccag
||||  | || ||||||||||||||||| || || |||||||||||||||   |||||||| || ||| |  | || ||||| || |||||| | |||||||||||||        | | || ||     ||| | ||      ||   |||| |||    || || ||  | |  | |   | |   | |   | |  |   |                                                                          
TTGCTTTGATTTTTTGGGAAACAAGGCGGTCTGATTTTGGAGTGTCAATGGGTCATCATGTGGCAACTTTTATTCTCATTGTGCTGTCTTACATATTCAGgtatgtttg-------gcagaagttcagcttgtagcttggcatgttctgaacaccataaccatgaggatgtgggttcataccaatttacctatttaaagtaaaacag-----------------------------------------------------------------------

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|86465981|gb|DY232354.1|DY232354

EST:     ATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAG                         ATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGATGT
genomic: ATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAGgtatgtttct ... cgtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGATGT

EST: gi|78085862|gb|DV514255.1|DV514255

EST:     TCACATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAG                         ATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGATGT
genomic: TCACATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAGgtatgtttct ... cgtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGATGT

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: 47 (upstream exon), 47 (downstream exon)
Score: 106

TTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTGTCAATGTCACATCATGTTGCTACTGTCGTCCTGATTGTTCTATCTTACGTGTTCAGgtatgtttct ... cgtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGATGTTTTCCTGGAAGTAGGGAAGATGTCCAAGTACAGTCATTGTGATTGGCTT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 171

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 170