ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTGCTTACAGCAGGACAAGGACATTGAATATTGGGGCATTGACTTCCAATCCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgctataccctgttcgcttaattttcttctgaatttctgataactttgaaaatactaattagtgcctctcttagctcagtttgcattccagttatcgacactaggagcacctgacctcttctacatgcatgcttacggttgcttgtttgcag

Basic information

species	Zea mays
transcript	GRMZM2G000660_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G000660_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g02180.1 (Oryza sativa), 5'ss of exon 2

TTGCTTACAGCAGGACAAGGACATTGAATATTGGGGCATTGACTTCCAATCCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgctatac-cctgttcgcttaattttcttctgaatttctgataactttgaaaatactaattagtgcctctcttagctcagtttgcattccagttatcgacactaggagcacctgacctcttctacatgcatgcttacggttgcttgtttgcag
|||||||||||||||||||||||||||||||||||||||||| |||||| |  ||||||||||||||||||||||||||||  | |||||||| |||||||||||     |||     |  |    || | |  | || |||||       |||   |||| || | |    |     | |||  | ||| |||| |   | || |                                                      
TTGCTTACAGCAGGACAAGGACATTGAATATTGGGGCATTGATTTCCAAACTGTTGTCAATAGGTGCAAAGAACTTGGCATAAAACACATCAGAAGACCGgtgagacgattatttatgtactgagctagtatcatgcttaattt------gcttatgaaattctgactcaaacaaaaatgagc--attttacatttctactttcaagc----------------------------------------------------

upper sequence: GRMZM2G000660_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g02120.2 (Oryza sativa), 5'ss of exon 4

TTGCTTACAGCAGGACAAGGACATTGAATATTGGGGCATTGACTTCCAATCCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgctatac-cctgttcgcttaattttcttctgaatttctgataactttgaaaatactaattagtgcctctcttagctcagtttgcattccagttatcgacactaggagcacctgacctcttctacatgcatgcttacggttgcttgtttgcag
|||||||||||||||||||||||||||||||||||||||||| |||||| |  ||||||||||||||||||||||||||||  | |||||||| |||||||||||     |||     |  |    || | |  | || |||||       |||   |||| ||  ||    |      |    || ||| ||||||   | || |                                                      
TTGCTTACAGCAGGACAAGGACATTGAATATTGGGGCATTGATTTCCAAACTGTTGTCAATAGGTGCAAAGAACTTGGCATAAAACACATCAGAAGACCGgtgagacgcttatttatgtactgagctagtatcatgcttaattt------gcttatgaaattctgcttcaaacaaaaaatgag-cactttacattcctactttcaag-----------------------------------------------------

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|76290166|gb|DV029734.1|DV029734

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|76920052|gb|DV167984.1|DV167984

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|211492251|gb|FL110847.1|FL110847

EST:     CATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGT
genomic: CATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACC-Ggtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGT

EST: gi|89253115|gb|DY624901.1|DY624901

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|33467334|gb|CF244383.1|CF244383

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|93283004|gb|EB675268.1|EB675268

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|89253066|gb|DY624852.1|DY624852

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|71302332|gb|DR787284.1|DR787284

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|71311577|gb|DR792164.1|DR792164

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGTCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|71312902|gb|DR792973.1|DR792973

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|78105236|gb|DV523654.1|DV523654

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|71426637|gb|DR807687.1|DR807687

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|76290165|gb|DV029733.1|DV029733

EST:     ATAGGTGC-AAGAAAC-TGGCATTTCAGCACATCAGGAGCCCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: ATAGGTGCAAAG-AACTTGGCA-TTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|78075798|gb|DV504232.1|DV504232

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|60345940|gb|DN212913.1|DN212913

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

EST: gi|76927038|gb|DV171123.1|DV171123

EST:     CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCG                         GCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT
genomic: CCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTT

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), 24 (downstream exon)
Score: 19

TTGCTTACAGCAGGACAAGGACATTGAATATTGGGGCATTGACTTCCAATCCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgc ... ttgtttgcagGCCGTGGATTTTGATCCAGACTCACTGAGGTCGCAACTGCCGAAAGCAGTTTCGGCGCTAGAATGGGCTACGTCGCAGCGCAAAGGGCGGGTTTATGTCC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 38

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 12

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTTACAGCAGGACAAGGACATTGAATATTGGGGCATTGACTTCCAATCCATTGTCAATAGGTGCAAAGAACTTGGCATTCAGCACATCAGGAGACCGgtgagcttgctataccctgttcgcttaattttcttctgaatttctgataactttgaaaatactaattagtgcctctcttagctcagtttgcattccagttatcgacactaggagcacctgacctcttctacatgcatgcttacggttgcttgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA