ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCACCCAAGCACTACTACGTCCAGGTCGACACCGGCAGCGACATCCTCTGGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGGgtaccatttccccccttttccccttttctgtgtgcctgaactgcagattaatttagttgtctccattttttgatgtgaattgcggtgtgtgggcgtctccgtgcag

Basic information

species	Zea mays
transcript	AC190609.3_FGT004
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC190609.3_FGT004 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g26834.1 (Oryza sativa), 5'ss of exon 2

GCCACCCAAGCACTACTACGTCCAGGTCGACACCGGCAGCGACATCCTCTGGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGGgtaccatttccccccttttccccttttctgtgtgcctgaactgcagattaatttagttgtctccattttttgatgtgaattgcggtgtgtgggcgtctccgtgcag
|||  ||||||  |||||||| ||||| |||||||||||||||||||||||||| ||||||||| ||||||| | |||||| | ||||||||| ||||||||| ||   |  | | ||| |  || |   | |    ||  |   ||||   | |  |||   ||         ||    ||| |                     
GCCGACCAAGCGGTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTGAACTGCATCTCCTGCGATCGATGCCCACGCAAGAGCGGCCTCGGGgtaacacaccatctcgttttcttttcttcttcttttagatttttggattctctcaactgtgggcaaaaccgtgcgttgcgtgcag---------------------

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|78077746|gb|DV506178.1|DV506178

EST:     GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGG                         TTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG
genomic: GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGGgtaccatttc ... ctccgtgcagTTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG

EST: gi|76021072|gb|DT948242.1|DT948242

EST:     GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGG                         TTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG
genomic: GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGGgtaccatttc ... ctccgtgcagTTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG

EST: gi|91874605|gb|EB404562.1|EB404562

EST:     GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGG                         TTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG
genomic: GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGGgtaccatttc ... ctccgtgcagTTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG

EST: gi|31360897|gb|CD445254.1|CD445254

EST:     GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGG                         TTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG
genomic: GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGGgtaccatttc ... ctccgtgcagTTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG

EST: gi|71767997|gb|DR965934.1|DR965934

EST:     GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGG                         TTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG
genomic: GGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGGgtaccatttc ... ctccgtgcagTTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTG

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: 45 (upstream exon), 49 (downstream exon)
Score: 24

GCCACCCAAGCACTACTACGTCCAGGTCGACACCGGCAGCGACATCCTCTGGGTCAACTGCATCACCTGCGAGCAATGCCCCCACAAGAGCGGGCTCGGGgtaccatttc ... ctccgtgcagTTAGACTTGACGCTTTACGACCCCAAGGCATCCTCGACCGGGAGCATGGTGATGTGCGATCAGGCATTCTGTGCAGCCACCTTTGGCGGAAAGCTGCCGA

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 52

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 17