ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...caaaacgttgcatctgctcatcttcatcttttttttgttctttaattcgaggacttactggtgtgtgctattcctttgcctgagttcatgttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCCCCTCCACACATGAAGATGTTATATGACAAAGCTTCTGATCATAACAGAA

Basic information

species	Zea mays
transcript	GRMZM2G412888_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G412888_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g41730.2 (Oryza sativa), 3'ss of exon 6

caaaacgttgcatctgctcatcttcatcttttttttgttctttaattcgaggacttactggtgtgtgctattcctttgcctgagtt-catgttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCCCCTCCACACATGAAGATGTTATATGACAAAGCTTCTGATCATAACAGAA
||     | |   ||  |   |     | |  |  ||| | ||| |     | ||   || ||||| |  ||| | |||  |  |  | | ||| ||||||||||||||||||||| | |||||||||||||| ||||||||| |||| |||||| ||||||||| | |  ||||||| ||||||| ||| ||||| |  |
cactttttggttactattttaccgagacctgatgctgtgcgtta-tctattgcctagttgatgtgtccctttcttatgctcgcttaaccttttcctcgcagGTCAAACAACCCATTATTTTCCTTTCTGGATTACAAGATGAATTAGTTCCCCCTTCACACATGAGGTTACTATATGAAAAAGCTTTTGAGCATAATAAGA

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|71427907|gb|DR808957.1|DR808957

EST:     TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAG                         GTCAAACAACCCCATTCTCTTCCTTTCTGGAT
genomic: TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCC-ATTCTCTTCCTTTCTGGAT

EST: gi|71425139|gb|DR806558.1|DR806558

EST:     TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAG                         GTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC
genomic: TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC

EST: gi|110195540|gb|EC877437.1|EC877437

EST:     TACACTTGATATTGTTGGAGAGG                         GTCAAACAACCCATTCTCTTTCCTTTTTGGATTGCAAGATGAACTAGTCC
genomic: TACACTTGATATTGTTGGAGA-Ggtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTC-TTCCTTTCTGGATTGCAAGATGAACTAGTCC

EST: gi|71448310|gb|DR829360.1|DR829360

EST:     TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAG                         GTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC
genomic: TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC

EST: gi|71427906|gb|DR808956.1|DR808956

EST:     TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAG                         GTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC
genomic: TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC

EST: gi|31997570|gb|CD661661.1|CD661661

EST:     TTGATATTGTTGGAGAG                         GTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC
genomic: TTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC

EST: gi|211038058|gb|FL324597.1|FL324597

EST:     TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAG                         GTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC
genomic: TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC

EST: gi|8103365|gb|AW928006.1|AW928006

EST:     TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAG                         GTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC
genomic: TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC

EST: gi|71316273|gb|DR794813.1|DR794813

EST:     TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAG                         GTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC
genomic: TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC

EST: gi|30705914|gb|CD058968.1|CD058968

EST:     ACTGTGTTGTTCGCTCTCCAT-GAATACCCTTGATATTGTTGGAGAG                         GTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC
genomic: ACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCC

EST: gi|91055111|gb|EB165529.1|EB165529

EST:     TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAG                         GTCAAACAACCCATTCTCTTCCTTTCTGGGAT-GCAAGATGAACTAGTCCC
genomic: TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGG-ATTGCAAGATGAACTAGTCCC

EST: gi|67041292|gb|CO467547.1|CO467547

EST:     TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGNTGGAGAG                         GTCAAACAACC-ATTCTCTTCCTTTCTGGNAT-GCA-GATGA-CTAGTCCC
genomic: TAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGG-ATTGCAAGATGAACTAGTCCC

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: 259

CTTCTTAAGATGGTTCATAGGCGGGAGCTCTTCTAAAGGTCCAAAACTTTTAAACTGTGTTGTTCGCTCTCCATGGAATACACTTGATATTGTTGGAGAGgtgagctttt ... ttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCCCCTCCACACATGAAGATGTTATATGACAAAGCTTCTGATCATAACAGAA

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 250

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcgaggacttactggtgtgtgctattcctttgcctgagttcatgttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCCCCTCCACACATGAAGATGTTATATGACAAAGCTTCTGATCATAACAGAA

      gacttac  putative branch site (score: 268)

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaacgttgcatctgctcatcttcatcttttttttgttctttaattcgaggacttactggtgtgtgctattcctttgcctgagttcatgttcatcgcagGTCAAACAACCCATTCTCTTCCTTTCTGGATTGCAAGATGAACTAGTCCCCCCTCCACACATGAAGATGTTATATGACAAAGCTTCTGATCATAACAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - -gcatctg
- - - - - - - - - - -cttcatc
- - - - - - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - actggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcatg