ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACTAGGGGACACAATATTAGGTCCTGAAGAAAATATTAGGTCCATTTCTAAGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttctttcgaattctggaagtttgtagatgttgattattcttgagcactgagcagagttgtaatttttttgttatgctgtctggtctag

Basic information

species	Zea mays
transcript	GRMZM5G827505_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G827505_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g51390.1 (Oryza sativa), 5'ss of exon 2

ACTAGGGGACACAATATTAGGTCCTGAAGAAAATATTAGGTCCATTTCTAAGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttctttcgaattctggaagtttgtagatgttgattattcttgagcactgagcagagttgtaatttttttgttatgc-tgtctggtctag
 || || ||||||||||||||||||| ||| |||||||  || || ||||||||||||||||||||||| ||  ||||||||||||||||||||||||||||| || |     | |   ||| |||  ||   ||||||  |  | | |    |    |||  | | | |||| || ||| ||  |||| |||
GCTGGGTGACACAATATTAGGTCCTGTAGAGAATATTAAATCGATCTCTAAGAAAGATTTGGAGCAATACATTACAACTCACTATACCTGTCCTCGAATGgtacttgtcagccagttctgaaatttacaggcattgatttgttatcaccgagcattctagtgctgaatgttttattttgcctggttggtttag

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|148945033|gb|EC890217.2|EC890217

EST:     AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATG                         GTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAAGTG
genomic: AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAAGTG

EST: gi|6031387|gb|AW076244.1|AW076244

EST:     AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATG                         GTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAAGTG
genomic: AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAAGTG

EST: gi|148983190|gb|EE029136.2|EE029136

EST:     GAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAAATG                         GT-GTATCTGCTGCTGGAAGTGT
genomic: GAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAA-TGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGGAAGTGT

EST: gi|71430235|gb|DR811285.1|DR811285

EST:     GAAAGATTTGGAGCAATATATCTCAACTCACTATACCCTGTC-TCGAATG                         GTTGTATCTGCTGCTGG
genomic: GAAAGATTTGGAGCAATATATCTCAACTCACTATACC-TGTCCTCGAATGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGG

EST: gi|149009597|gb|EE041558.2|EE041558

EST:     AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATG                         GTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAAGTG
genomic: AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAAGTG

EST: gi|74244154|gb|DT652068.1|DT652068

EST:     AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATG                         GTTGTATCTGCTGCTGGGAGTGTCAGTCACGATGAGGTTGTTGATCAA
genomic: AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAA

EST: gi|91056228|gb|EB166646.1|EB166646

EST:     AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATG                         GGTGTATCTGCTGCTGGAA
genomic: AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGGAA

EST: gi|71436989|gb|DR818039.1|DR818039

EST:     AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATG                         GTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAAGTG
genomic: AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAAGTG

EST: gi|149078045|gb|EE166785.2|EE166785

EST:     AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATG                         GTTGTATCTGCTGCTGGA
genomic: AGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGGA

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: 45

ACTAGGGGACACAATATTAGGTCCTGAAGAAAATATTAGGTCCATTTCTAAGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttcttt ... tctggtctagGTTGTATCTGCTGCTGGAAGTGTCAGTCACGATGAGGTTGTTGATCAAGTGAAAGAATTATTCACAGAATTCTCCACTGATCCAACTACTGCTGATCAGC

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 69

Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 58

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 30

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTAGGGGACACAATATTAGGTCCTGAAGAAAATATTAGGTCCATTTCTAAGAAAGATTTGGAGCAATATATCTCAACTCACTATACCTGTCCTCGAATGgtatttctttcgaattctggaagtttgtagatgttgattattcttgagcactgagcagagttgtaatttttttgttatgctgtctggtctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA