ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagctgcaagcgtggtaactaataaacatgtggtatttatgcgtcaaagtaaactaatctgttaattttcaatctgtgaaataatatttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAAGGATATTGACTGGCTTCCTAGATCTCCTGAGCCTATGAGTGGTTCCTAT

Basic information

species	Zea mays
transcript	GRMZM2G020775_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G147041_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g49320.1 (Oryza sativa), 3'ss of exon 2

gtaagctgcaagcgtggtaactaataaacatgtggtatttat----gcgtcaaa-------gtaaactaatctgttaatt-------ttcaatctgtgaaataatatttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAAGGATATTGACTGGCTTCCTAGATCTCCTGAGCCTATGAGTGGTTCCTAT
||||| |  || |     |   |||||||||    | ||| |    | || | |        ||||  |  | ||| |||       |||||| ||| |  |||| |||  |||||||||||||||| ||||| || |||||||||||| |||||||||||||||| |||| ||| ||||||||| ||||||||||| |||| |  |||||||||
gtaagttctaatccccaaacaaaataaacatacaatctttcttcttgtgttagatattctgataaataagccagttgattatctctattcaatttgtcatgtaatgttt--gcagAGGGCTGACCCACTTTGATGTTGACAACTTTGTTCAAGAAGTGCTTGTGAAAGATACTGAATGGCTTCCTGGATCTCCTGAGGCTATAAAAGGTTCCTAT

upper sequence: GRMZM2G147041_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 2

gtaagctgcaagcgtggtaactaataaacatgtggtatttatgcgtcaaagtaaac--taatctgttaattttcaatctgtgaaataatatttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAAGGATATTGACTGGCTTCCTAGATCTCCTGAGCCTATGAGTGGTTCCTAT
             ||  ||   | | || || ||   || |||  ||  | |||||  |||    ||  ||  |||| |   ||| |       |||||| || |||| |||||||| |||||||  |||||||| || ||||||||||||| | |||| ||| | ||| ||  ||||||  || | ||| |||| |||
-------------gtactactcagttaatat-tgtggttgatgattcttaataaacggtaactcatt--ttggcaatttcaaaaaaa-------tgcagAAGGTTGACTCATTTTGATGTGGACACATTTGTTGAGGAGGTGCTTGTGAAGGGTGTTGAGTGGTTGCCTGGAAATCCTGAATCTCTTAGTAGTTCATAT

upper sequence: GRMZM2G147041_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv19s0015g00750.t01 (Vitis vinifera), 3'ss of exon 2

-gtaagctgcaagcgtggtaactaataaacatgtggtatttatgcgtcaaagtaaactaatctgttaattttcaatctg--tgaaataatatttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAAGGATATTGACTGGCTTCCTAGATCTCCTGAGCCTATGAGTGGTTCCTAT
   ||  | |||   || |    | |    ||| | |  |  ||    | | |           ||||   | | | ||  |  | ||| |    |||||  |  |||| |||||||| || ||||  ||||||||||||||||| |||||||||  ||| ||||  |||  | |||||||     | | ||| || |  
gtcaaattacaattctgtttga-atttgttatg-gatgctcttgtagaatactttttcccctgcttaacactaattatggttttagtaa-agaaatgcagGAGATTGACGCATTTTGATGTTGACACATTTGTTGAAGAAGTGCTCGTGAAGGATGGTGAGTGGCAGCCTGTAACTCCTGAAAAACTAATTGGGTCATGC

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|74232969|gb|DT640883.1|DT640883

EST:     GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAA                         AGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA
genomic: GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAAgtaagctgca ... atttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA

EST: gi|19057851|gb|BM736518.1|BM736518

EST:     GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAA                         AGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA
genomic: GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAAgtaagctgca ... atttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA

EST: gi|211389154|gb|FL356157.1|FL356157

EST:     TCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAA                         AGGGCTGACCCATTTTGATGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA
genomic: TCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAAgtaagctgca ... atttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA

EST: gi|211066678|gb|FL084208.1|FL084208

EST:     GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAA                         AGGGCTGACCCATTTTGATGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA
genomic: GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAAgtaagctgca ... atttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA

EST: gi|211066679|gb|FL084209.1|FL084209

EST:     GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAA                         AGGGCTGACCCATTTTGATGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA
genomic: GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAAgtaagctgca ... atttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA

EST: gi|211500207|gb|FL084206.1|FL084206

EST:     GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAA                         AGGGCTGACCCATTTTGATGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA
genomic: GAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAAgtaagctgca ... atttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA

EST: gi|211059299|gb|FL363871.1|FL363871

EST:     TCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAA                         AGGGCTGACCCATTTTGATGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA
genomic: TCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAAgtaagctgca ... atttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 79

ATCAAATTGACCATCTGTGAAGGAGAAGATGGCACTGAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAAgtaagctgca ... atttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAAGGATATTGACTGGCTTCCTAGATCTCCTGAGCCTATGAGTGGTTCCTAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 138

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcgtcaaagtaaactaatctgttaattttcaatctgtgaaataatatttttgcagAGGGCTGACCCATTTTGACGTGGACAACTTTGTTGAAGAAGTGCTTGTGAAGGATATTGACTGGCTTCCTAGATCTCCTGAGCCTATGAGTGGTTCCTAT