ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGGTGTGGGCCATGCCGTGTCATTGCTCCTGTCTATGCTGAAATGTCAAAGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaatcttacatgtgccaaattagtttttggaattatgcatggcttcgacttagggcatgtttggaagtacctagtttttaagaaactggtttat...

Basic information

species	Zea mays
transcript	GRMZM2G066612_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G066612_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g07690.1 (Oryza sativa), 5'ss of exon 4

CTGGTGTGGGCCATGCCGTGTCATTGCTCCTGTCTATGCTGAAATGTCAAAGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgta-tttcaatcttacatgtg-ccaaattagtttttggaattatgcatggcttcgacttagggcatgtttggaagtacctagtttttaagaaactggtttat
||||||||| ||||| ||||| ||||| ||| | |||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||| ||  || | |   | ||  |||||| | | ||| ||  |||  |   |||   || |          |||   |||  |   |  ||    |||  ||
CTGGTGTGGACCATGTCGTGTTATTGCACCTATTTATGCTGAGATGTCAAAGACTTATCCTCAACTCATGTTCTTGACAATAGATGTTGATGACCTAATGgtaattctaaccgtttgtttggtcaaatttgctattgaaaa-atgattaatttcagttttgtatgaaccaagaaaccccttatacatctgatggcggtc-at

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|44900360|gb|CK826905.1|CK826905

EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC

EST: gi|211449385|gb|FL478319.1|FL478319

EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACGTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC

EST: gi|84977611|gb|DW476033.1|DW476033

EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC

EST: gi|17932304|gb|BM269264.1|BM269264

EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC

EST: gi|18180492|gb|BM381702.1|BM381702

EST:     TCCTCAACTCATGTTCTTGGCAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: TCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC

EST: gi|7162522|gb|AW520144.1|AW520144

EST:     AGACTTATCCTCAACTCATGTTCTTGCCAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC

EST: gi|28984394|gb|BQ539056.2|BQ539056

EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC

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), 49 (downstream exon)
Score: 127

CTGGTGTGGGCCATGCCGTGTCATTGCTCCTGTCTATGCTGAAATGTCAAAGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 471

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 467