ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TAGTTCAATGGTAGTGGATGGCTCATTTGTATCATCTATGTCCTCTGATAACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatgggttactagttttctttttgatttcttttaatttcccatatagcataaactctagcctacagcagtacagccccttcattttgttattgcaa...

Basic information

species	Zea mays
transcript	GRMZM2G093096_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G093096_T04 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g27019.5 (Oryza sativa), 5'ss of exon 7

TAGTTCAATGGTAGTGGATGGCTCATTTGTATCATCTATGTCCTCTGATAACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatgggttactagttttctttttgatttcttttaatttcccatatagcataaac-tctagcctacagcagtacagccccttcattttgttattgcaa
 |  ||||||||||| ||||| || || ||||| ||||| || |||||||||||||| ||||| | ||||||||  || || |||||||| |||||||||||||    | ||| |  | | |  | || |   |||||   |     ||    || |  | |    ||        |   | | | ||||  || | || |
CACCTCAATGGTAGTTGATGGGTCCTTCGTATCGTCTATTTCTTCTGATAACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagtttattt-tctgcaatgtggtccattttatggttgtgcatgaactacatatttgatatatctttcctccagctcgtaatttaattctagcga

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|6021401|gb|AW066329.1|AW066329

EST:     ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAG                         CTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA

EST: gi|32849606|gb|CD989287.1|CD989287

EST:     TGCTGTTAGTCAG                         CTGGATGTGCAACCCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: TGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA

EST: gi|60352422|gb|DN219395.1|DN219395

EST:     ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAG                         CTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA

EST: gi|60338470|gb|DN205443.1|DN205443

EST:     ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAG                         CTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA

EST: gi|67026168|gb|CO454917.1|CO454917

EST:     CACGTCGAAGAAAGCAGCTTTTCA-CAACTGGCAG-ATGCTGTTAGTCAG                         CTGGATGTGCAAACCAAAT
genomic: CA-GTCGAAGAAAGCAGCTTT-CAACAACTG-CAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAAT

EST: gi|166654720|gb|EG090357.1|EG090357

EST:     AAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAG                         CTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: AAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA

EST: gi|60354452|gb|DN221425.1|DN221425

EST:     ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAG                         CTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA

EST: gi|67041729|gb|CO467984.1|CO467984

EST:     ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAG                         CTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA
genomic: ACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCA

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: 236

TAGTTCAATGGTAGTGGATGGCTCATTTGTATCATCTATGTCCTCTGATAACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatggg ... tctacttcagCTGGATGTGCAAACCAAATTGTGCATCAGGGATGGTTTATACCGATTGGCACGAAGTGCGCAACATAGACAAGTTTTTCCAAATACGATGAACAGCAATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGTTCAATGGTAGTGGATGGCTCATTTGTATCATCTATGTCCTCTGATAACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatgggttactagttttctttttgatttcttttaatttcccatatagcataaactctagcctacagcagtacagccccttcattttgttattgcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT