ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGAGTTCAATTTCCGCTGGACCCGCCGCAGCCTCGCCGTCGTCGGCCTCTTCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatccactatagcgagcccctcttgtcgttccactgtccctttcccctttctccaaaccctaagataaattttctgtttgttcctgctg

Basic information

species	Zea mays
transcript	GRMZM2G004111_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G004111_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G15610.1 (Glycine max), 5'ss of exon 1

CGAGTTCAATTTCCGCTGGACCCGCCGCAGCCTCGCCGTCGTCGGCCTCTTCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatccactatag-cgagcccct--------cttgtcgttccac-tgtccctt---tcccctttctccaaaccctaagata------aattttctgtttgttcctgctg-------------------------------------------------------------
 |||||||||||||| ||||| ||||||| ||| ||  | || ||| |||||||| ||||| | ||| ||||||||||||||||||||||||| ||||||||||      ||   | |   ||         ||| || ||| || | | | ||   | |  ||||| |   |  || | ||       ||||||  ||| ||    |                                                               
GGAGTTCAATTTCCGTTGGACTCGCCGCAACCTTGCTCTTGTTGGCATCTTCGGCATCGCTATTCCCGTCCTCGTCTACAAGGGCATCGTCCGTGAATTCgtaagtagtcattttccaattcccaattagggcttttcattctacctatgcattcgattctttttcttccttctttatgttatacttggattttcactttcttttaacaactatatctctccttctgctgaaacatgttttattttcaaaaacaatcaatttctgattcag

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|211261975|gb|FK957247.1|FK957247

EST:     TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         GGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG
genomic: TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatccact ... gttcctgctgGGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG

EST: gi|211343055|gb|FL473796.1|FL473796

EST:     TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         GGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG
genomic: TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatccact ... gttcctgctgGGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG

EST: gi|78027010|gb|DV495397.1|DV495397

EST:     TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         GGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG
genomic: TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatccact ... gttcctgctgGGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG

EST: gi|211261976|gb|FK957248.1|FK957248

EST:     TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         GGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG
genomic: TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatccact ... gttcctgctgGGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG

EST: gi|211261974|gb|FK957246.1|FK957246

EST:     TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         GGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG
genomic: TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatccact ... gttcctgctgGGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG

EST: gi|4826238|gb|AI667866.1|AI667866

EST:     TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         GGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG
genomic: TCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatccact ... gttcctgctgGGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAG

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: 12 (upstream exon), 48 (downstream exon)
Score: 2

CGAGTTCAATTTCCGCTGGACCCGCCGCAGCCTCGCCGTCGTCGGCCTCTTCGGCCTCGCTGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatccact ... gttcctgctgGGTTGGATCCAGCATATGCAGGACGAGGATGCAGGCCGGCCATACAGGAAGTTCCTGTAAGCGGCGTCCAGGGCTGCAGGAGACGTCGATCCCTCGACCG

Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 6

Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 6