ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcctgtttgtgataatcggataatgaagtgaatcatgcatttcctcattataaaccgatgattctgtttttctgctgtcag

Basic information

species	Zea mays
transcript	GRMZM2G477146_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G477146_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g31874.2 (Oryza sativa), 5'ss of exon 10

GCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcctgtttgtga-taatcggataatgaagtgaatcatgcatttcctcattataaaccgatgattctgtttttctgctgtcag
 |||||  | |||||||||||||||||||||||||||||||| |||||||||||||| || |||||||| ||||||||||| |||||||||||||||||||| |||| |||||||| | || |    |||  | | ||||| ||  || | |||| ||||||  | | || ||  || |     | ||
CCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTGTGTACTTTCAAGAATATCAAgtgagtttctgtttgtaaatattatcgtaagcatgagaatcttgtgttgc-tcatgataaactaagggttttggattgccttcattag

upper sequence: GRMZM2G477146_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA02G07510.2 (Glycine max), 5'ss of exon 11

GCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcctgtttgtgataatcggataatgaagtgaatcatgcatttcctcattataaaccgatgattctgtttttctgctgtcag-----------------
 |||||||| ||||||||||| || |||||||| |||||||| || || ||||| || ||||| || |||||||||||| | || |||||||||||||| |||  ||||| |||    | ||   | |   | ||      ||| |||| |    |      || ||||   |  |  |  ||                     
ACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAGCATGGACTTTGTTCTCAATATGTACAGGATTTATATATTTTCAAGAATATCAGgtac-ttcctctttaacttgat---acacacaggtagcctttgcctttcatgggcactctaagaagatttaatcatattattgaagaaaactaattaaatatca

upper sequence: GRMZM2G477146_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA16G26550.1 (Glycine max), 5'ss of exon 11

GCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcctgtttgtgataatcggataa-tgaagtgaatcatgcatttcctcattataaaccgatgattctgtttttctgctgtcag------------
 |||||||| ||||||||||| || |||||||| |||||||| ||  | ||||| |||||||| || |||||||||||| | || |||||||||||||| |||  |||    |      |   | | |  |    |      |||||   | |  ||  ||    | ||  | |  |  ||  |  |             
ACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAACATGGACTTTCTTCTCAATCTGTACAGGATTTATCTATTTTCAAGAATATCAGgtactttctctctcacttaatatgcacaggtagcctttgctttgcatgggcactctaagaagatttaatcatataatattgaagaaaactaattaaatac

upper sequence: GRMZM2G477146_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT3G26670.1 (Arabidopsis thaliana), 5'ss of exon 10

GCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttc-ctgtttgtgataatcggataatgaagtgaatcatgcatttcc---tcattataaacc--gatgattctgtttttc-tgctgtcag--------------------------------------------------------
  ||||  ||| ||||||||| || || |||||||||||||| ||||||||||| |||||||| || ||||||||||   ||||||||||||| | ||| ||   |    ||  |    |     | |  |    |   |  |  || | |     | ||   | |  |||||||   ||  || |  |||||                                                         
ATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCATTTACTTTCAAGAGTTTCAGgttcatctattgactacattgtgatgcttttcctctcttttctttatcttcgggctaatacggatctagatgattagtttgatcattttgtcacagaatggtgtgggtttagggatagtcgcttagataattttcttcttccttaaacag

upper sequence: GRMZM2G477146_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv14s0068g00780.t01 (Vitis vinifera), 5'ss of exon 10

GCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttc-------ctgtttgtgataatcggataatgaagtgaatcatgcatttcctcattataaaccgatgattctgtttttctgctgtcag------
| ||||||| ||||||||||| || |||||||| |||||||||||||||||||| |||||||||||||||||||||||||| |||||||| |||||||| ||    ||       || | | |     |   | ||   ||||| | |    ||  || |    ||   |       | |  || |||||          
GTTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAAATTGCTTGGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAGgtgctctctctctctctctctctctctcttatagaacctagtgactgaaaatttaacttaggtcaatttggctccattttacttgtgctgctcactggga

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|6056444|gb|AW090954.1|AW090954

EST:     GGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAA                         GTATTTGATACGCTCAGGATAATTATGTTTGTGTTAGGCATGACATTTGTC
genomic: GGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcct ... ctgctgtcagGTATTTGATACGCTCAGGATAATTATGTTTGTGTTAGGCATGACATTTGTC

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: 77

GCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTGTTTACTTTCAAGAATATCAAgtaagttcct ... ctgctgtcagGTATTTGATACGCTCAGGATAATTATGTTTGTGTTAGGCATGACATTTGTCTTTGTTGGGATTTCCTTGCTAGCACCCGATGACAGTAAAG

Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 37

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62