ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtactgatactatctatcatctgatgctgtctgttttggtcgaaccgtagcttgcatgctcaccatggatcgccatctgttccagGAAAAGCAGCGGCTTCTCGCGCGGCGCTTCGATCTACCGGGGAGTCACCAG

Basic information

species	Zea mays
transcript	GRMZM2G028151_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G028151_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 5

--gtactg-ata-ctatctatcatctgatgctgt--ctgttttggtcgaaccgtag--cttgcatgc-tcaccatggatcgccatctgttccagGAAAAGCAGCGGCTTCTCGCGCGGCGCTTCGATCTACCGGGGAGTCACCAG
    ||||  || ||| |||| |  |      ||  |||          |  ||    ||  |||   | | | |  ||  |  | || | |||||||||||| ||||||||||| ||||||||||||||||| |||||||||||
gtacactgcgtagctacctatgaaatcgccaagtcactgaacgaacaagattgtgacactgacatctgtaaacctccatgtctgtttgctgcagGAAAAGCAGTGGCTTCTCGCGTGGCGCTTCGATCTACCGTGGAGTCACCAG

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|76012118|gb|DT939288.1|DT939288

EST:     GAGGAGATGAAGAACATGACCAGACAGGAGTACGTCGCTCACCTGAGAAG                         GAAAAGCAGCGGCTTCTCGCGCGGCGCTTCGATCTACCGGGGAGTCACCAG
genomic: GAGGAGATGAAGAACATGACCAGACAGGAGTACGTCGCTCACCTGAGAAGgtactgatac ... tctgttccagGAAAAGCAGCGGCTTCTCGCGCGGCGCTTCGATCTACCGGGGAGTCACCAG

EST: gi|78092257|gb|DV520631.1|DV520631

EST:     GAGGAGATGAAGAACATGACCAGACAGGAGTACGTCGCTCACCTGAGAAG                         GAAAAGCAGCGGCTTCTCGCGCGGCGCTTCGATCTACCGGGGAGTCACCAG
genomic: GAGGAGATGAAGAACATGACCAGACAGGAGTACGTCGCTCACCTGAGAAGgtactgatac ... tctgttccagGAAAAGCAGCGGCTTCTCGCGCGGCGCTTCGATCTACCGGGGAGTCACCAG

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 1 RNA-Seqlibrary.

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 96

GTGGAGGACTACAGGGAAGAGCTGGAGGAGATGAAGAACATGACCAGACAGGAGTACGTCGCTCACCTGAGAAGgtactgatac ... tctgttccagGAAAAGCAGCGGCTTCTCGCGCGGCGCTTCGATCTACCGGGGAGTCACCAG

<

<

<

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgttttggtcgaaccgtagcttgcatgctcaccatggatcgccatctgttccagGAAAAGCAGCGGCTTCTCGCGCGGCGCTTCGATCTACCGGGGAGTCACCAG