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

gtaaggattttgttttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAGTCAGCGTTGAAGGGCTCCCACT

Basic information

species	Zea mays
transcript	GRMZM2G702490_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G702490_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 4

gtaaggattttgttttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAGTCAGCGTTGAAGGGCTCCCACT
||||| ||||| ||    |  ||   ||     ||| | | ||  |||| ||||| ||| || ||  ||| |||  ||||| ||||||||||||||| |||||||||||||||||||| ||||| || ||||||||||||||||||||||||||||||||||||||||| |||||  | ||||| |||||||
gtaagtattttctt----attcttgactaa-gcttgtagtctgtatcttgtgcatcgtgtaagtcgttttctttaactttacatttatgcagACACTGGTGACTGGTTTTGCAAGGATTTGTGGACAGCCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAATCAGCCCTAAAGGGTTCCCACT

upper sequence: GRMZM2G702490_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G14860.1 (Glycine max), 3'ss of exon 4

------gtaaggattttgttttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaa---tttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAGTCAGCGTTGAAGGGCTCCCACT
         |  | |    | |  ||    |||    |     |       |   || |  | | |   | | | |    |  ||| ||   ||| |||||||||| ||||| || ||||| || || | ||| || || ||||||||||||||||||||||| ||||| || |  || || ||  |||| ||  |||| |
aaaatttctacaactcatctatataccagtagcctggaagaaaagcgcagttgcaattccctat-ctgtttattataaccttttttgaaatctttttgcagACACTTGTGACAGGATTTGCTAGAATTTTTGGACAGCCTGTTGGAATTATTGGAAACAATGGGATTTTATTCAATGAATCTGCACTGAAAGGGGCCCATT

upper sequence: GRMZM2G702490_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G33620.1 (Glycine max), 3'ss of exon 4

gtaaggattttgttttggacactcagctgt-catttgcattttgcgtcttatgcattgt-gcaactca-atttgttt---------tcctttaaat--ttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAGTCAGCGTTGAAGGGCTCCCACT
      ||    |||     ||||| | ||  | | | |   ||      | ||   || |||| ||  || |||||         |  || ||||  || |||||||||| ||||| || ||||| || || |  || || || ||||||||||||||||||||||| ||||| || |  || || ||  |||| ||  |||| |
------ataaaatttctacaactcatcagtatactggtagcctggaagaaaagcgcagttgcaattcctatctgtttattataacctttttgaaatctttttgcagACACTTGTGACAGGATTTGCTAGAATTTTCGGACAGCCTGTTGGAATTATTGGAAACAATGGGATTTTATTCAATGAATCTGCACTGAAAGGGGCCCATT

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|211125173|gb|FL001723.1|FL001723

EST:     TCAAAAAATTGTATGGAACA                         ACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT
genomic: TCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT

EST: gi|60341832|gb|DN208805.1|DN208805

EST:     GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACA                         ACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT
genomic: GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT

EST: gi|211125174|gb|FL001724.1|FL001724

EST:     GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACA                         ACACTAAGTGGACTGGGTTTGCAAGGGATATGTGGGCAACCAGTTGGAA
genomic: GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTA-GTG-ACTGGTTTTGCAAGG-ATATGTGGGCAACCAGTTGGAA

EST: gi|211125176|gb|FL001726.1|FL001726

EST:     GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACA                         ACACTAGTGACTGGTTTTGCA
genomic: GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTAGTGACTGGTTTTGCA

EST: gi|71430320|gb|DR811370.1|DR811370

EST:     GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAA---T-T------                         ACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT
genomic: GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT

EST: gi|18164072|gb|BM333911.1|BM333911

EST:     TGAGTTCAAAAAATTGTATGGAACA                         ACACTAGTGACTGG-TTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT
genomic: TGAGTTCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT

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: 46 (upstream exon), 48 (downstream exon)
Score: 93

TGCACCAGCTGATGTGAAACAGTCCTTCGACATTCGTTCAATAATAGCCCGTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAGTCAGCGTTGAAGGGCTCCCACT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 410

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 125

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAGTCAGCGTTGAAGGGCTCCCACT

                            aatttgttttccttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggattttgttttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATTGGAAACAATGGCATTTTGTTTACAGAGTCAGCGTTGAAGGGCTCCCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG