ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtttgttcctgccattttcatttgtcatgtttccatttcctggatctggagccgaataagctgacaaaattcccttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATACAGTGTACAACTTCTTCGTTTACCGGGAACCATTGTACATAGATAATGCT

Basic information

species	Zea mays
transcript	GRMZM2G126601_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G126601_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g43860.1 (Oryza sativa), 3'ss of exon 8

--------------------------gtttgttcctgccattttcatttgtcatgtttccatttcctggatctggagccgaataagctgacaaaattcccttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATACAGTGTACAACTTCTTCGTTTACCGGGAACCATTGTACATAGATAATGCT
                           || |||  |      | | ||   | | ||   | ||  |      |  || | |||| | |   | ||    ||    ||| || ||||||||||||||||| ||||||||||||||||||||| | || ||| |||||||||  || || |||| | | ||  |||||||||| ||||||
gtacatttctgcacatctcctctccaattagttgttcatgcctaccttcaaccttttgtaaatttatcttatcgaggcgggataaacggt--atatcttatttccacagCAATTCGGTGAACATATATGTCGGCATTGGTGTTCCATGGTTGGTGGACACAATGTACAACTATTTTGTCTACCAGAAGCCCCTGTACATAGACAATGCT

upper sequence: GRMZM2G126601_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G02250.1 (Glycine max), 3'ss of exon 7

---------------gtttgttcctgccattttcatttgtcatgt--ttccatttcctggatctggagccgaataagctgacaaaattcccttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATACAGTGTACAACTTCTTCGTTTACCGGGAACCATTGTACATAGATAATGCT
                    |   |  | || | | ||| ||  |  ||   | |  ||     |  |   | |||  |    |  |   ||| ||| || || || ||||| ||||||||||| ||||||||||||||| | ||||||||  ||||||||||| | |  ||  | |||||  |    ||  | ||||| 
atgaagcatagatgaaaccatcagttgctttatgacttgccaaatcattttttgttttgatgaagttggttattaacttcgttatttattctttttgtagCAATTCAGTGAATATATATGTTGGTATTGGTGTTCCATGGCTTATTGATACTTTGTACAACTTCATAGCATATAGAGAACCTCTCCGAATCCAAAATGCA

upper sequence: GRMZM2G126601_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT2G47600.1 (Arabidopsis thaliana), 3'ss of exon 8

gtttgttcctgccattttcatttgtcatgtttccatttcctggatctggagccgaataagctgacaaaattcccttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATACAGTGTACAACTTCTTCGTTTACCGGGAACCATTGTACATAGATAATGCT
         |   | | |||     | | |    |  |    |||||      ||      ||   | |     |    ||||||||||||||||||| ||||| || ||||| ||||| ||| ||||  | ||||| ||||||| ||| |  ||| | || || || |||||||| || |||
--------gtaaaaatctcaaa-accctttacaaacattgaagatcttttcatgatctttttggtgataaattat----gcagTAACTCGGTGAACATCTATGTGGGGATTGGAGTTCCGTGGCTGATAAACACAGTCTACAACTACTTTGCATACAGAGAGCCTTTATACATAGAAAACGCT

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|8383342|gb|BE056285.1|BE056285

EST:     GCTGAGCGTCAAGTCACCGCGGACTCTGCAATAGCCAACATCACTTGCAG                         TAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATAC
genomic: GCTGAGCGTCAAGTCACCGCGGACTCTGCAATAGCCAACATCACTTGCAGgtttgttcct ... cttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATAC

EST: gi|32807621|gb|CD959855.1|CD959855

EST:     GCTAAGCGTCAAGTCACCGCGGACTCTGCAATAGCCAACATCACTTGCAG                         TAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATAC
genomic: GCTGAGCGTCAAGTCACCGCGGACTCTGCAATAGCCAACATCACTTGCAGgtttgttcct ... cttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATAC

EST: gi|32808198|gb|CD960432.1|CD960432

EST:     GCTGAGCGTCAAGTCACCGCGGACTCTGCAATAGCCAACATCACTTGCAG                         TAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATAC
genomic: GCTGAGCGTCAAGTCACCGCGGACTCTGCAATAGCCAACATCACTTGCAGgtttgttcct ... cttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATAC

EST: gi|78179857|gb|DV550230.1|DV550230

EST:     GCTGAGCGTCAAGTCACCGCGGACTCTGCAATAGCCAACATCACTTGCAG                         TAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATAC
genomic: GCTGAGCGTCAAGTCACCGCGGACTCTGCAATAGCCAACATCACTTGCAGgtttgttcct ... cttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATAC

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

CACTGGCCGCTGGAACCTCATGGCCAGATCTAGTTGCTAGCAAGATAGCTGCTGAGCGTCAAGTCACCGCGGACTCTGCAATAGCCAACATCACTTGCAGgtttgttcct ... cttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATACAGTGTACAACTTCTTCGTTTACCGGGAACCATTGTACATAGATAATGCT

Block sizes: 44 (upstream exon), 36 (downstream exon)
Score: 8

Block sizes: 44 (upstream exon), 38 (downstream exon)
Score: 13

Block sizes: 42 (upstream exon), 43 (downstream exon)
Score: 20

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtttccatttcctggatctggagccgaataagctgacaaaattcccttgttgcagTAACTCGGTGAACATATATGTTGGCATTGGTGTTCCATGGTTGATTGATACAGTGTACAACTTCTTCGTTTACCGGGAACCATTGTACATAGATAATGCT