ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ATCATATTTTCTACATCTTCACTGGCTTTGCCTGGTACTTTGGCACGGTTTTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatcttgatttctagttcattgaaatttctacttttttcaggagaatgccaagctcatgaattattttttcacaaactgagccgaattttaattttctgctgtag

Basic information

species	Zea mays
transcript	GRMZM5G809546_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G809546_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g15460.2 (Oryza sativa), 5'ss of exon 6

ATCATATTTTCTACATCTTCACTGGCTTTGCCTGGTACTTTGGCACGGTTTTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatcttgatttctagttcatt-gaaatttctacttttttca-ggagaatgccaagctcatgaattattttttcacaaactga--gccgaattttaattttctgctgtag
|| |||||||||||||||||  ||||||||||||||||||||||||| ||| |||||||||| |||||||| |||||||||||| |||| |||||||||||||||| |      | | || ||| || ||||||| |  | |||  | ||   ||| |||    ||  |   ||| ||  ||     |   |    | |||| ||  ||||| ||
ATAATATTTTCTACATCTTCTTTGGCTTTGCCTGGTACTTTGGCACGATTTACTGGCTTAGAGTTTCTTAAAAAGGCTGCCATATCCCTAAATCCAGGAGgtaaacaaggagtttctataattcttttgaaatttgttgtctttatatgggagatggcaatgcaatagacattttgtttgcatgtaaatcactttctgttaacttcatgctgcag

upper sequence: GRMZM5G809546_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0065g00940.t01 (Vitis vinifera), 5'ss of exon 6

ATCATATTTTCTACATCTTCACTGGCTTTGCCTGGTACTTTGGCACGGTTTTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatcttgatttctagttcattgaaatttctacttttttcaggagaatgccaagctcatgaattattttttcacaaactgagccgaattttaattttctgctgtag
||||||||||||||||| ||| ||||| | ||||||||| || |||| ||| |||| ||||     || |||||||||||  | ||  | ||||| || |||||   |   || | |   ||| | ||  |     |  || ||    ||| | |  |         | ||||| |   | | | |  |    | ||   | | |   || 
ATCATATTTTCTACATCATCATTGGCTCTTCCTGGTACTGTGTCACGCTTTACTGGATTAGCTGCACTAAAGAAGGCTGCATTGGCTTTAAATCCTGGGGgtaagtaac--tgttctactgtt-actggtac----aagttgttagacagagtacataatcttcctctaattttattcaatattcaatca---tgtatactacaggcata-

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|71315712|gb|DR794487.1|DR794487

EST:     TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|60353250|gb|DN220223.1|DN220223

EST:     ATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: ATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|94473420|gb|EB702378.1|EB702378

EST:     TTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|149099085|gb|EE185105.2|EE185105

EST:     TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|148951011|gb|EC896663.2|EC896663

EST:     TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|149098781|gb|EE184792.2|EE184792

EST:     TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|86475140|gb|DY241510.1|DY241510

EST:     T-TGGCTTAGACTTTCTTAAGAAGGCTGCCAATAGCCCTTAATCCAGGAG                         GTGCTCTTTTTCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TCTGGCTTAGACTTTCTTAAGAAGGCTGCC-ATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|148936039|gb|EC880097.2|EC880097

EST:     CTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|211175781|gb|FL245446.1|FL245446

EST:     ACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: ACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|5901117|gb|AW042217.1|AW042217

EST:     TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|149101790|gb|EE187903.2|EE187903

EST:     TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|32942308|gb|CF047127.1|CF047127

EST:     TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

EST: gi|71426546|gb|DR807596.1|DR807596

EST:     TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAG                         GTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT
genomic: TTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATT

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), 47 (downstream exon)
Score: 88

ATCATATTTTCTACATCTTCACTGGCTTTGCCTGGTACTTTGGCACGGTTTTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatc ... tctgctgtagGTGCTCTCTATCTTCCAACTAATGTATTACTTATAGCCTTCTTCAACTATTATTACACGTTTCTCCAGTTAGATCCTGATGATCTTAGTGAACAATTGAA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 221

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

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATATTTTCTACATCTTCACTGGCTTTGCCTGGTACTTTGGCACGGTTTTCTGGCTTAGACTTTCTTAAGAAGGCTGCCATAGCCCTTAATCCAGGAGgtaaactatcttgatttctagttcattgaaatttctacttttttcaggagaatgccaagctcatgaattattttttcacaaactgagccgaattttaattttctgctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG