ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTGGCGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcagttcgtttttagtgtatcgatggatgcatgaaggcatgtttaattgaattccaatccatgtcttattctgagccacttgcag

Basic information

species	Zea mays
transcript	GRMZM2G110289_T01
intron #	16
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G110289_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os06g13050.1 (Oryza sativa), 5'ss of exon 17

CGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTGGCGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcagttcgtttttagtgtatcgatggatgcatgaaggcatgtttaattgaattccaatccatgtcttattctgagccacttgcag
 || |||||||| ||||||||||| || || || ||||| || ||||| || ||||| ||||||||||| ||||||||||||||||| ||||| |||||||| || |     |||      ||  |      || ||||  | ||| || | ||   ||  | | |||| ||  ||  ||| || | ||||
TGATGGAGCATTTGCATTGGCACAAGCACTTAAAGCTAATGAAGATCTTGCAGTCACATCATTAAATCTTGCAAACAACTTCTTCACTAAATTTGGACAGgtcagttg---ccgtaccagttggct------attcatggtgtcat-ttgagttatgtttta-ttcatg-ctggtt--gagtcaat-gcag

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|60354010|gb|DN220983.1|DN220983

EST:     CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAG                         GTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG
genomic: CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcag ... ccacttgcagGTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG

EST: gi|67010636|gb|CO439385.1|CO439385

EST:     CGGTCACGTCATTAAATCTCGCANACAACTTCTTCACGAAATTCGGACAG                         GTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG
genomic: CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcag ... ccacttgcagGTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG

EST: gi|71763770|gb|DR961707.1|DR961707

EST:     CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAG                         GTCGCTCTTTTTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG
genomic: CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcag ... ccacttgcagGTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG

EST: gi|60355903|gb|DN222876.1|DN222876

EST:     CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAG                         GTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG
genomic: CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcag ... ccacttgcagGTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG

EST: gi|166682496|gb|EG164862.1|EG164862

EST:     GTCACGTCGTTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAG                         GTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG
genomic: GTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcag ... ccacttgcagGTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG

EST: gi|32937038|gb|CF041857.1|CF041857

EST:     CGGTCACGTCATTAAATCTCGCAAACAACTTTTTCACGAAATTCGGACAG                         GTCGCTCTTTTTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG
genomic: CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcag ... ccacttgcagGTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG

EST: gi|60341143|gb|DN208116.1|DN208116

EST:     CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAG                         GTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG
genomic: CGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcag ... ccacttgcagGTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAG

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), 49 (downstream exon)
Score: 122

CGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTGGCGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGACAGgttagatcag ... ccacttgcagGTCGCTCTTTCTGAGGCGCGGGACCATGTGTACGAGATGACCGAACGGGAGATAGACATTTATTTTTAGGGGGGTACCGGTTCCCCTGTGCACACAGTTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125