ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGGAGTTGCCATCTCGGAAAATTATAACTCCTCTGAAGGATATTGGACTGGGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAGgtattctactaccactaccatccttgtatcgtttctcacaattctgactgacaatgtttgtggtatagcag

Basic information

species	Zea mays
transcript	GRMZM2G140726_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G140726_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g35700.1 (Oryza sativa), 5'ss of exon 10

GGGAGTTGCCATCTCGGAAAATTATAACTCCTCTGAAGGATATTGGACTGGGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACA------Ggtatt----ctactaccactaccatccttgtatcgtttctcacaattc-tgactgacaatgt-ttgtggtatagcag
       |   ||  |||||| ||| ||||| || |||||||| ||| || |    ||||||||||| |||||||||||  | ||||||||||||||||      |||| |     |  | |   || | ||  | | |  | |||  ||| |  |   ||   |||| || |  || |||||
------AGTTCTCAAGGAAAAGTATCACTCCCCTAAAGGATATAGGAGTGAGTGCAAGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgattcttgcatttatcctcactttgtactctctttcaacttgttgatgcttatgtattatcctacagcag

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|74235693|gb|DT643607.1|DT643607

EST:     GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAG                         TCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAG
genomic: GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAGgtattctact ... ggtatagcagTCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAG

EST: gi|76920827|gb|DV168328.1|DV168328

EST:     ATTTTCCACTACTGTTCCTTCACCACACAG                         TCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAG
genomic: ATTTTCCACTACTGTTCCTTCACCACACAGgtattctact ... ggtatagcagTCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAG

EST: gi|33092164|gb|CF052158.1|CF052158

EST:     GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAG                         CAGCCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTC
genomic: GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAGgtattctact ... ggtatagcagT--CC-TATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTC

EST: gi|13316055|gb|BG410502.1|BG410502

EST:     GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAG                         TCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAG
genomic: GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAGgtattctact ... ggtatagcagTCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAG

EST: gi|78025110|gb|DV493497.1|DV493497

EST:     GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAG                         TCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAG
genomic: GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAGgtattctact ... ggtatagcagTCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAG

EST: gi|74235692|gb|DT643606.1|DT643606

EST:     GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAG                         TCCTATTCCTGGAAGAGCAAACATGTTTACGCCAGTTTCACCATGCTCAAG
genomic: GGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAGgtattctact ... ggtatagcagTCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAG

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: 43 (upstream exon), 48 (downstream exon)
Score: 23

GGGAGTTGCCATCTCGGAAAATTATAACTCCTCTGAAGGATATTGGACTGGGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACAGgtattctact ... ggtatagcagTCCTATTCCTGGAAGAGCAAACATGTCTACGCCAGTTTCACCATGCTCAAGCCCGCTGCGGCAGTTTAAGCAATCCAATGTGAGGGGCATGCGTTCTCCA

Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 46

Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 45