ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatctcctccatattctgatttttttgatttcatgaatttctttcccatttgttggagcttatcatcgtgccttatgttagttttgtctaacttg...

Basic information

species	Zea mays
transcript	GRMZM2G111511_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G111511_T05 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g56400.1 (Oryza sativa), 5'ss of exon 4

TGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatctcctccatattctgattttt--ttgatttcat--gaatttctttcccatttgttggagcttatcatcgtgccttatgttagttttgtctaacttg
 |||||||| ||||||||||||||||| ||||| ||||||||||||||||||||| |||| ||||| || |||||||||||||| |||||| | |||||||| | ||| |  | ||| ||||  ||| |  |   ||  |    |||       ||| || ||         | | ||   || | | ||    || | |    
CGGGCAGAAGCAGAGAGTTGCAATTGCCGGTGCTTTAGCTGAAGCATCCAAAGTACTACTACTGGATGAGCTGACCACATTCTTGGATGAATACGACCAGgtataaatataatgcatgttcttgtttctaatcagttgtactcaaatactccctccactttttaatatacgacgttgttgattttttgagaaacgtttga----

upper sequence: GRMZM2G111511_T05 (Zea mays), 5'ss of exon 2
lower sequence: AT4G33460.1 (Arabidopsis thaliana), 5'ss of exon 4

TGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatctcctccatattctgatttttttgatttcatg-aatttctttcccatttgttggagcttatcatcg-tgccttatgttagttttgtctaac--ttg
||| |||||||| ||| |||| ||||||||||| ||||||||||| | ||||||  || || |||| || || || || ||| |||||||   |||||||||  |  | |  |  ||  |   |   |  | ||   |   || |  | |  ||      | | | |  |||   ||   ||| | |   | | |  |   |||
TGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAACTTTCCTAGATGAGTCTGACCAGgtaagg-tttgattaattctaacaacgtgctaatgaaacacaactagtattgca---agggaacccttccataactggaatatttcaacatcgacatatgattg

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|18173493|gb|BM348881.1|BM348881

EST:     AAGTATTAGTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|211373270|gb|FL465535.1|FL465535

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|17931952|gb|BM268912.1|BM268912

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|211053231|gb|FL127757.1|FL127757

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|60394524|gb|DN227394.1|DN227394

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|14243054|gb|BG840773.2|BG840773

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|18169738|gb|BM339578.1|BM339578

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|71434457|gb|DR815507.1|DR815507

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|32866994|gb|CF006676.1|CF006676

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTAATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|74238567|gb|DT646481.1|DT646481

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|18165876|gb|BM335715.1|BM335715

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|17932020|gb|BM268980.1|BM268980

EST:     AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

EST: gi|71434456|gb|DR815506.1|DR815506

EST:     AAGTATTACTGCTGGACGAACTGACCCCATTTTTAGATGAACATGACCAG                         ATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC
genomic: AAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTC

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: 47 (upstream exon), 43 (downstream exon)
Score: 15

TGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatct ... gcaactgcagATAGGCGTGATAAATGCAGTGAGGGACTCTGTGGCTGCCGATGGGGAGGTCGCCGCATTATGGGTGACTCATCGGTTGGAAGAGCTGAAATATGCAGATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 27

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 22

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 26

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCACATTCTTAGATGAACATGACCAGgtttgaatctcctccatattctgatttttttgatttcatgaatttctttcccatttgttggagcttatcatcgtgccttatgttagttttgtctaacttg

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