ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGGCGGCAACATTACCACCGTCGAGCGCCCCGAGGAAGGGTACCTCTGGGAGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcctcgctggcgccgcagcgtcttcttctcagactcatgcggagccatggaattgagatgctgaatggattttatgcgcgcgcgcag

Basic information

species	Zea mays
transcript	GRMZM2G039396_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G039396_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g18320.1 (Oryza sativa), 5'ss of exon 1

CGGCGGCAACATTACCACCGTCGAGCGCCCCGAGGAAGGGTACCTCTGGGAGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacg-ctcctcgctggcgccgcagcgtcttcttctcagactcatgcggagccatggaattgagatgctgaatggattttatgcgcgcgcgcag
|||||||||||| ||||||| ||||||| |||  || || ||||||||||||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||| || || |||  | ||    | |||  |||||   |    | |  | |||| ||| |  ||| ||  || ||    || | ||||||||
CGGCGGCAACATCACCACCGCCGAGCGCGCCGGCGAGGGCTACCTCTGGGAGGAGGGGCCCAACAGCTTCCAGCCTTCCGACCCCGTCCTCACCATGGCCgtacgtcttcttgct--ccccttctcttctgattctctcgcggcggagacgacatg-aatgggaatggtgg-tgcatggattggg-gcgcgcag

upper sequence: GRMZM2G039396_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv07s0005g02540.t01 (Vitis vinifera), 5'ss of exon 1

------CGGCGGCAACATTACCACCGTCGAGCGCCCCGAGGAAGGGTACCTCTGGGAGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcctcgctggcgccgcagcgtcttcttctcagac-tcatgcggagccatggaattgagatgctgaatggatttt----atgcgcgcgcgcag---
       || ||||| || |||||| | |||      | ||| || || ||||||||||| || |||||||||||||||||||||||  || | ||||||||||||||| | |    ||   |  |   |  ||     | ||    | ||        || | ||     | ||   |  |||      ||    ||  |||    
TCGCGTTGGGGGCAATATAACCACCATGGAG------GGGGACGGCTATCTCTGGGAGGAAGGCCCCAACAGCTTCCAGCCCTCCGATTCCATGCTCACCATGGCCgtaagttttgagcct-catctgggtttcactgacccacttattatctccgttgataggatcatattccttcttatattcccaccatttctgcttgcaatgc

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|149005349|gb|EE039900.2|EE039900

EST:     AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCC                         GTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG
genomic: AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcct ... gcgcgcgcagGTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG

EST: gi|149071120|gb|EE159520.2|EE159520

EST:     AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCC                         GTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG
genomic: AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcct ... gcgcgcgcagGTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG

EST: gi|78079002|gb|DV507414.1|DV507414

EST:     AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCC                         GTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG
genomic: AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcct ... gcgcgcgcagGTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG

EST: gi|211265727|gb|FL016769.1|FL016769

EST:     AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCC                         GTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG
genomic: AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcct ... gcgcgcgcagGTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG

EST: gi|211265725|gb|FL016767.1|FL016767

EST:     AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCC                         GTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG
genomic: AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcct ... gcgcgcgcagGTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG

EST: gi|211265723|gb|FL016765.1|FL016765

EST:     AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCC                         GTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG
genomic: AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcct ... gcgcgcgcagGTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG

EST: gi|78087541|gb|DV515934.1|DV515934

EST:     AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCC                         GTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG
genomic: AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcct ... gcgcgcgcagGTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG

EST: gi|211265728|gb|FL016770.1|FL016770

EST:     AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCC                         GTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG
genomic: AGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcct ... gcgcgcgcagGTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCG

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: 48 (upstream exon), 47 (downstream exon)
Score: 132

CGGCGGCAACATTACCACCGTCGAGCGCCCCGAGGAAGGGTACCTCTGGGAGGAGGGTCCCAACAGCTTCCAGCCCTCCGACCCCGTTCTCACCATGGCCgtacgctcct ... gcgcgcgcagGTGGACAGCGGACTGAAGGATGACTTGGTTTTTGGGGACCCAAACGCGCCGCGTTTCGTGCTGTGGGAGGGGAAGCTGAGGCCCGTGCCATCCAAGCCCG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 212

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 54