ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAAGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacctcctcgcctccctaatctaaaaaaaactactcttttttacgtcctcgtgggtactcgaggttgtggtgcatttctaatgtggtaagagcaa...

Basic information

species	Zea mays
transcript	GRMZM2G032419_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G032419_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g37080.1 (Oryza sativa), 5'ss of exon 2

CACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAAGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct--cctcgcctccctaatctaaaaaaaactactctttttta---cgtcctcgtgggtactcgaggttgtggtgcattt---ctaatgtggtaagagcaa
 || ||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||| |||  ||||  | ||||| || |   |    |  ||||    |   |  |||  |   | ||  ||||| || ||  ||       ||||||         
GACGAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTACCTCCAGAACAAGACCCAGATCGGCAAGGTCGACGAGATCTTCGGCCCCATCAACGAATCCgtgagctcctctcctcctccccctactccactcattcttgatcttgaagaatccaacctttttcttgcttcaggttttgttgagttcaggtagatgtggc--------

upper sequence: GRMZM2G032419_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv08s0007g07410.t01 (Vitis vinifera), 5'ss of exon 2

CACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAAGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacctcctcgcctccc-taatctaaaaaaaactactcttttttacgtcctcgtgggtactcgaggttgtggtgcatttctaatgtggtaagagcaa
||| || | |||| | |||||||| || || || || ||||||||||||||||||||||| || || ||||| || ||||||||||||||||| || || ||||| | |       ||||   | | ||      | |  |  ||| ||  || |  | |||  ||  || | || |  | ||||  | |  | |  ||| 
CACAAATGCGAAGATACCCTACTTTAATGCTCCAATTTATCTGCAGAACAAGACCCAGATAGGGAAAGTTGATGAAATCTTCGGCCCCATCAATGAGTCTgtgagtagccagcgttctcctacattttattctctagttttggtttgtagatcatgtttggt--tcaggggtttgatctagttcttgttttattatggcag

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|31357816|gb|CD442173.1|CD442173

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211457053|gb|FL081470.1|FL081470

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211003881|gb|FL081488.1|FL081488

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|60344900|gb|DN211873.1|DN211873

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|29130259|gb|CB380963.1|CB380963

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211454925|gb|FL081458.1|FL081458

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211454927|gb|FL081460.1|FL081460

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211003875|gb|FL081482.1|FL081482

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211457047|gb|FL081464.1|FL081464

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCYATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211003882|gb|FL081489.1|FL081489

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGG-ATCATTG
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTG

EST: gi|60343373|gb|DN210346.1|DN210346

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211457061|gb|FL081478.1|FL081478

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAAC
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAAC

EST: gi|211003885|gb|FL081492.1|FL081492

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211457056|gb|FL081473.1|FL081473

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211003883|gb|FL081490.1|FL081490

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGA

EST: gi|211457048|gb|FL081465.1|FL081465

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTTGCAACATCGTACAATGA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATT-GCAACATCGTACAATGA

EST: gi|211454926|gb|FL081459.1|FL081459

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACMTCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211457057|gb|FL081474.1|FL081474

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

EST: gi|211454928|gb|FL081461.1|FL081461

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGT
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGT

EST: gi|211003874|gb|FL081481.1|FL081481

EST:     AGACCCAGATCGGCMAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGC
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGC

EST: gi|211457060|gb|FL081477.1|FL081477

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGG
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGG

EST: gi|211454930|gb|FL081463.1|FL081463

EST:     GACCCAGATCGGCAAGGTTGAAGAGATCCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTAC
genomic: GACCCAGATCGGCAAGGTTGAAGAGATC-TTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTAC

EST: gi|211003872|gb|FL081479.1|FL081479

EST:     AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCC                         TATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA
genomic: AGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAA

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: 315

CACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAAGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacct ... gtatgtgtagTATTTCTCTGTGAAGATGATGGAGGGGATCATTGCAACATCGTACAATGAAGGCGACAAGTTCTATATCGACCCAATGAAATTGCTGCCGCTCTCACGCT

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 49

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 93

Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 60

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAAGACCCAGATCGGCAAGGTTGAAGAGATCTTCGGCCCCATCAACGAATCCgtgagcacctcctcgcctccctaatctaaaaaaaactactcttttttacgtcctcgtgggtactcgaggttgtggtgcatttctaatgtggtaagagcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaaa