ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...tgcaactctcctgcatattcgagaaaaaaagttgtgagcctgacaccctgtgatgatgtataatgacttcgaactaagaaacttttctcttatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCTGGAATGAAGTTTATATCTTCTGCCGTTGTGTCCTCAGTGTTGAGATGCT

Basic information

species	Zea mays
transcript	GRMZM5G817035_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G817035_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g40630.1 (Oryza sativa), 3'ss of exon 3

tgcaactctcctgcatattcgagaaaaaaagttgtgagcctgacaccctgtgatgatgtataatgacttcgaactaa--gaaacttttctcttatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCTGGAATGAAGTTTATATCTTCTGCCGTTGTGTCCTCAGTGTTGAGATGCT
  || |||       |  |          ||   ||          ||||  || |  | || ||| || || || |   || |||     || |||   |||| ||||| |||||||||||||| || ||||||||||| || ||||||||||||||||||||| |||| |||||  |||||||||| ||| |||||||||
--cagctcgtgctattgctattttctggtagccatggaggactgggcctgcaataacctgtattgattttgagctcaccaaagcttgctcattgtttgctagGTACTTGCGCTAGCATATTATGCTATTTCATACTTCCCCGGGGGATCTGCTGGAATGAAGTTTCTATCATCTGCACTTGTGTCCTCTGTGCTGAGATGCT

upper sequence: GRMZM5G817035_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0057g01380.t01 (Vitis vinifera), 3'ss of exon 3

--tgcaactctcctgcatattcgagaaaaaaagttgtgagcctgacaccctgtgatgatgtataatgacttcgaactaagaaacttttctcttattttt-cagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCTGGAATGAAGTTTATATCTTCTGCCGTTGTGTCCTCAGTGTTGAGATGCT
  |     |||| |   |  | || | ||  | || |    ||    ||   |  |  | |    ||| || |    |   ||    |   | || ||   |||||||||| ||  | |||||||| || || ||||||||||| ||||||||||||||||||||| | |||||  |  |    || |   | |||| ||| |
tatcatgatctcttctgtgat-gatacaaggaattct--ttctctttcctgattttattttgacttgatttagtggaacttaatcccttcttaatgttggtagGTCCTTGCGCTCTCTTATTATGCTATTTCCTACTTCCCTGGAGGATCTGCTGGAATGAAGTTTCTGTCTTCAACTCTGACCTCTTTGATATTGAAATGTT

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|211224884|gb|FL455738.1|FL455738

EST:     CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAG                         GTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT
genomic: CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT

EST: gi|149040600|gb|EE046841.2|EE046841

EST:     CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAG                         GTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT
genomic: CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT

EST: gi|211310097|gb|FL216550.1|FL216550

EST:     CAATGGTGCTTCATAGCTACATACTTTCTGTYTTCTKCTCTGTGCTTCAG                         GTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCT
genomic: CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCT

EST: gi|78082562|gb|DV510974.1|DV510974

EST:     CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAG                         GTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT
genomic: CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT

EST: gi|71425789|gb|DR806892.1|DR806892

EST:     CAATGGTGCTTCATAGCTACATACTTTCTGNNNNNNNCTCTGTGCTTCAG                         GTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT
genomic: CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT

EST: gi|74236298|gb|DT644212.1|DT644212

EST:     CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAG                         GTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT
genomic: CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT

EST: gi|211310098|gb|FL216551.1|FL216551

EST:     CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTYCTCTGTGCTTCAG                         GTCCTTGCTCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT
genomic: CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT

EST: gi|74236299|gb|DT644213.1|DT644213

EST:     CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAG                         GTCCTTGCCCTAGCATATTATGCCCTCTCATACTTCCCTGGTGGATCTGCT
genomic: CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT

EST: gi|71425790|gb|DR806893.1|DR806893

EST:     CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAG                         GTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT
genomic: CAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCT

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), 45 (downstream exon)
Score: 56

ACCTTTCACCATGGGATTTGTCGGGAGCATGGTTGCTACGATCTACGTGTCAATGGTGCTTCATAGCTACATACTTTCTGTTTTCTTCTCTGTGCTTCAGgtgataacac ... tatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCTGGAATGAAGTTTATATCTTCTGCCGTTGTGTCCTCAGTGTTGAGATGCT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 32

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

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 40

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ccctgtgatgatgtataatgacttcgaactaagaaacttttctcttatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCTGGAATGAAGTTTATATCTTCTGCCGTTGTGTCCTCAGTGTTGAGATGCT

                                    cttttctcttattttt  CT-rich tract
                                     ttttctcttattttt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaactctcctgcatattcgagaaaaaaagttgtgagcctgacaccctgtgatgatgtataatgacttcgaactaagaaacttttctcttatttttcagGTCCTTGCCCTAGCATATTATGCCATCTCATACTTCCCTGGTGGATCTGCTGGAATGAAGTTTATATCTTCTGCCGTTGTGTCCTCAGTGTTGAGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
tgcaact
- - - -ctcctgc
- - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - -ctgacac
- - - - - - - - - - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaactaa