ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTCgtgagtataatatgagcaccgcattctgtttgacgaaatttatttttctgcattttagttaaatttgagatgtttttaaggcttatcgtactttctaaat...

Basic information

species	Zea mays
transcript	GRMZM2G085577_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G085577_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g63270.1 (Oryza sativa), 5'ss of exon 4

AAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTCgtgagtataatatgagcaccgcattctgtttgacgaaatttatttttctgcattttagttaaatttgagatgtttttaaggcttatcgtactttctaaat-------------------
|| |||||||| ||||| |||  |||||||||  | || | |||  |||||||||||||||| |||||||||||||| ||||| |||| |||| ||           |||| | || ||  |  || | |  |         |||||||| ||| ||   | ||  |||| |  | |  || | ||                   
AAGTTCAGCCCATGGGAAATTGTCAGGCATGACATTGTATACCCAATCAGATTTTTTGGCCACGTTGAGATTTTGCCAGATGGATCgtaagtacaa-------gttccatttttttagaaaatgttgactaat---------agttaaatatgacat---tatatagcttgtgttgccctccatattaaaaaaaaaaggtgcctg

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|148961830|gb|EE012612.2|EE012612

EST:     GTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC                         TCGGAAATTGGTCGGAGGAGAAGTCCTGAAGGCTTTAGCATATGATGTGCC
genomic: GTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTCgtgagtataa ... catgtgatagTCGGAAATTGGTCGGAGGAGAAGTCCTGAAGGCTTTAGCATATGATGTGCC

EST: gi|87155862|gb|DY400651.1|DY400651

EST:     GTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC                         TCGGAAATTGGTCGGAGGAGAAGTCCTGAAGGCTTTAGCATATGATGTGCC
genomic: GTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTCgtgagtataa ... catgtgatagTCGGAAATTGGTCGGAGGAGAAGTCCTGAAGGCTTTAGCATATGATGTGCC

EST: gi|22133496|gb|BQ833744.1|BQ833744

EST:     G-GTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC                         TCGGAAATTGGTCGGAGGAGAAGTCCTGAAGGCTTTAGCATATGATGTGCC
genomic: GTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTCgtgagtataa ... catgtgatagTCGGAAATTGGTCGGAGGAGAAGTCCTGAAGGCTTTAGCATATGATGTGCC

EST: gi|26558458|gb|CA830693.1|CA830693

EST:     G-GTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC                         TCGGAAATTGGTCGGAGGAGAAGTCCTGAAGGCTTTAGCATATGATGTGCC
genomic: GTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTCgtgagtataa ... catgtgatagTCGGAAATTGGTCGGAGGAGAAGTCCTGAAGGCTTTAGCATATGATGTGCC

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), 49 (downstream exon)
Score: 335

AAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTCgtgagtataa ... catgtgatagTCGGAAATTGGTCGGAGGAGAAGTCCTGAAGGCTTTAGCATATGATGTGCCAATCCCTGGATACAAGACAAAAAATGCAATCAGTCTTCGTCTTTGGGAA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 433

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88