ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGAACTAATGTGCAAGGAAGGTTTGCAATCACTTTTTCCCATGGAAGAAATTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatgtgtgtgtgtgcctcatcccttgctttctctttgtatgatgcacttgacattaattgtactcacttcaattctgcag

Basic information

species	Zea mays
transcript	GRMZM2G176699_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G176699_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g54900.1 (Oryza sativa), 5'ss of exon 2

TGAACTAATGTGCAAGGAAGGTTTGCAATCACTTTTTCCCATGGAAGAAATTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatgtgtgtgtgtg----cctcatcccttgctttctctttgtatgat--gcacttg-acattaattgtactcacttcaattctgcag
 ||| ||||| ||||  |||| ||||| ||||||||||||||||| |||||| |||| |||||  ||||||| |||||||| |||||||| | ||||||||| | |  |   | ||| |      ||||| | ||||||| | ||  | |  |  | ||||| |  |||||| | |||| ||   || | |||
GGAATTAATGCGCAATAAAGGCTTGCAGTCACTTTTTCCCATGGAGGAAATTTCCATAATGGGATTGTGGGAACTGCTGCCACACATATATAATATCAAGgtgcaatgttgttctgtctcatactctcatgctttgctttttgttcatgttctctggacttgtattttaattatgctcattttggttttacag

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|33468054|gb|CF245103.1|CF245103

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|89251960|gb|DY623746.1|DY623746

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|148934449|gb|EC878487.2|EC878487

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCACATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|78090762|gb|DV519136.1|DV519136

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|148947273|gb|EC892641.2|EC892641

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATCCAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCG
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCG

EST: gi|148934293|gb|EC878319.2|EC878319

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|71771081|gb|DR969018.1|DR969018

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|71439989|gb|DR821039.1|DR821039

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|31350639|gb|CD434996.1|CD434996

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|74244436|gb|DT652350.1|DT652350

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|71764590|gb|DR962527.1|DR962527

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|50334194|gb|CO529320.1|CO529320

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

EST: gi|93282885|gb|EB675149.1|EB675149

EST:     TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAG                         AGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT
genomic: TTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCT

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: 34 (upstream exon), 40 (downstream exon)
Score: 14

TGAACTAATGTGCAAGGAAGGTTTGCAATCACTTTTTCCCATGGAAGAAATTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatg ... aattctgcagAGGAAAATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCTGTGGTTACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAAC

Block sizes: 29 (upstream exon), 46 (downstream exon)
Score: 3

Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 9

Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 35

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAACTAATGTGCAAGGAAGGTTTGCAATCACTTTTTCCCATGGAAGAAATTGCCATTATGGGCATGTGGGAGCTGCTGCCGCACATATACAGTATCAAGgtactacatgtgtgtgtgtgcctcatcccttgctttctctttgtatgatgcacttgacattaattgtactcacttcaattctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC