ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AAAAAGCATGGAGGGGAAACCTTATGGGTATCACAATATGATATTTAGCTGGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgtatgattctacatgttcaactttgaagatcactttactgctaaacctgtttatatatgcgttgcatatcttgccctgtgtgttactgtagcttagatat...

Basic information

species	Zea mays
transcript	GRMZM2G139374_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g58114.2 (Oryza sativa), 5'ss of exon 4

AAAAAGCATGGAGGGGAAACCTTATGGGTATCACAATATGATATTTAGCTGGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgtatgattctacatgttcaactttgaagatcactttactgctaaacctgtttatatatgcgttgcatatcttgcc-ctgtgtgttactgtagcttagatat--
|||||||||||| || |||||||||||||| ||||||||||| ||||| |||||||||||||| || || || |||||||| ||||||||||||||||||||||||| | | ||       |   || | || ||| ||        | ||  ||  || | |  |||||||  | |  | | ||    |||  | | |    
AAAAAGCATGGATGGAAAACCTTATGGGTACCACAATATGATTTTTAGTTGGATTGATACCATAAGCGACAACTATCCACCGCCATTAGATGCTCATGTGgtatgat-caatatcactttttgccaacagcattttgctaacgcttatattattaagtgtgct--atatcttatcgccatatattttcataggctggttgctt

upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT4G27020.1 (Arabidopsis thaliana), 5'ss of exon 4

AAAAAGCATGGAGGGGAAACCTTATGGGTATCACAATATGATATTTAGCTGGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgtatgattctacatgttcaactttgaagatcactttactgctaaacct--gtttatatatgcgttgca-tatcttgccctgtgtgttactg--tagcttagatat-------------------------------------------------------
    |||||||| || ||||| ||||| ||||||||  |||| ||||||||||| ||||||||||| |  ||||| ||||| ||  | ||||||||  | ||| | ||  |  | |   | |||    ||   |       |||   |  |||||| | |   |||   | ||||        |  ||     ||| |||    |                                                       
TCGTAGCATGGATGGCAAACCATATGGCTATCACAACTTGATCTTTAGCTGGATCGATACCATCAGCGGAAATTACCCACCTCCTCTGGATGCTCAACTTgtaggttttcatttctcagaattttggcattgatgacaacataagtttcagtttatctctttattgttctctctttaatcagcttctatcagttagtttatgggtgaggttgtgattgttttctctgtatctcttttccttctctattatgtttttccag

upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G54870.1 (Arabidopsis thaliana), 5'ss of exon 4

AAAAAGCATGGAGGGGAAACCTTATGGGTATCACAATATGATATTTAGCTGGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgtatgattctacatgttcaactttgaagatcactttactgctaaacctgtttatatatgcgttgcatatcttgccctgtgtgttactgtagcttagatat
    ||||||||||| ||||| ||||| ||||||||  |||| ||||| |||||||||||| | ||||| || || || || ||  ||||||| ||| | ||| | || |   | ||||  | | |  ||    ||  || | ||    |  |  |     | |    | |  |   | |  |  || |   | ||    
TCGCAGCATGGAGGGTAAACCATATGGTTATCACAACTTGATTTTTAGTTGGATTGATACCGTTAGTGAAAACTACCCGCCTCCTCTAGATGCCCATCTTgtaagtttttgt-ttttcatttctcacaatatagttcttgatgaatgaatacactttcaaatcgt---tttaacttcgggcttctctttctttcag----

upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv19s0090g00100.t01 (Vitis vinifera), 5'ss of exon 4

AAAAAGCATGGAGGGGAAACCTTATGGGTATCACAATATGATATTTAGCTGGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgtatgattctacatgttcaactttgaagatcactttactgctaaacctgtttatatatgcgttgcatatcttgccctg---tgtgttactgtagcttagatat
|   |||||||| || ||||||||||| || || || ||||||||||||||||| ||| |  |   ||| || |||||||| || |||||||||||||||||||  || | | | |     ||   | || |    ||  |  |  |  || | | | | ||   | || || | | |   ||  ||| | |     || |  
ACGTAGCATGGAAGGCAAACCTTATGGTTACCATAACATGATATTTAGCTGGATAGATGCTCTGGATGAAAACTATCCACCCCCCTTAGATGCTCATGTGgtattgtttttc-tctattgtttctcaaattaagcaacaac--atgcaattaaaacaagagtcagaaatgtttctcagatttggattatttttttaaaggtgc

upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv19s0090g00130.t01 (Vitis vinifera), 5'ss of exon 4

AAAAAGCATGGAGGGGAAACCTTATGGGTATCACAATATGATATTTAGCTGGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgtatgattctacatgttcaactttgaagat--cactttactgctaaacctgtt-tatatatgcgttgcatatcttgccctgtgtgttactgtagcttagatat
|   ||||  || || ||||||||||| || || || ||||||||||||||||| |||||  |   ||| || |||||||| || |||||||||||||||||||  || |   | |  |   || || ||  || |||   |||| | |||   || |  ||  ||  |||| |       | | |  || || |||  | | 
ACGTAGCAGTGAAGGCAAACCTTATGGTTACCATAACATGATATTTAGCTGGATAGATACTCTGGATGAAAACTATCCACCCCCCTTAGATGCTCATGTGgtattgtttt---tttctattgttaaatatttcattttctggctacatctgcaatacaggtggattctatatttcttttcttttatctctatatctttcaaaa

upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 4
lower sequence: PP1S191_130V6.3 (Physcomitrella patens), 5'ss of exon 5

AAAAAGCATGGAGGGGAAACCTTATGGGTATCACAATATGATATTTAGCTGGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgta-tgattctacatgttcaactttgaagatc--actttactgctaaacctgtttatatatgcgttgcatatcttgccctgtg-tgttactgtag--cttagatat-----------------------------
     | |||   |||  ||||||||| ||||| || |||||||||||||||||||||||    |  ||||||||||| || ||  | ||  |  |  ||||| |  || |||||  |  ||  |     |   | |||         ||  || | |||||   || |       | |  || |  | |||||   |||  ||||                             
TCGTCGAATGAGTGGGGCACCTTATGGCTATCATAACATGATATTTAGCTGGATTGATACTCCGACCGATAATTATCCCCCTCCTCTCGACTCCAACTTGgtaatttttttacattattgacagtagtattttaaatttgtcaggtctccacttgagatatgacatgaaccgtggactcaatggtcgtcctgtacatcttgtatatgctaaatactaagctggtgttggtgacag

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|6918323|gb|AW399853.1|AW399853

EST:     GGATTGATACCATCAGTGATAATTATCCGCCACCATTAGATGCTCATGTG                         GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCT
genomic: GGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgtatgattct ... atgtccacagGTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCT

EST: gi|71311669|gb|DR792242.1|DR792242

EST:     GTGATAATTATCC-CCACCCATTAGATGCTCATGTG                         GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCT
genomic: GTGATAATTATCCACCA-CCATTAGATGCTCATGTGgtatgattct ... atgtccacagGTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCT

EST: gi|211364276|gb|FL199173.1|FL199173

EST:     GGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTG                         GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCT
genomic: GGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgtatgattct ... atgtccacagGTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCT

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: 156

AAAAAGCATGGAGGGGAAACCTTATGGGTATCACAATATGATATTTAGCTGGATTGATACCATCAGTGATAATTATCCACCACCATTAGATGCTCATGTGgtatgattct ... atgtccacagGTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 523

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 571