ERISdb: a Database of Plant Splice Sites

General
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AAGCCCAAGGAGCCGTACGTCGGGAGGTGCCTGCTCAACACCAGGATCACCGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagcttacctaattagtagcagtaatctagtgttagttaggataaggtaaggtgatgtattgggtggtcgtgcatgcag

Basic information

species	Zea mays
transcript	GRMZM2G059083_T01
intron #	1
splice site	5'
intron type	U2

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|78085945|gb|DV514338.1|DV514338

EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

EST: gi|89253046|gb|DY624832.1|DY624832

EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

EST: gi|605756|gb|T27568.1|T27568

EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATG-CG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

EST: gi|76015965|gb|DT943135.1|DT943135

EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

EST: gi|13490690|gb|BG517454.1|BG517454

EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

EST: gi|13557961|gb|BG549317.1|BG549317

EST:     CACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

EST: gi|13382263|gb|BG458938.1|BG458938

EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

EST: gi|13126400|gb|BG316970.1|BG316970

EST:     TGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: TGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

EST: gi|50328327|gb|CO523453.1|CO523453

EST:     GGCGACCAAGCGCCCGGGGAGACATGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: GGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

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: 45

AAGCCCAAGGAGCCGTACGTCGGGAGGTGCCTGCTCAACACCAGGATCACCGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324