ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

...tgtccaatgaaaaatagtcaagtgagatcctgtggatgcttactttctttccagttagtatgacattgtattgctataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA

Basic information

species	Zea mays
transcript	GRMZM2G112672_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 3

---------tgtccaatgaaaaatagtcaagtgag--atcctgtggatgcttactttctttccagttagtatgacattgtattgctataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA
           | |    || |  ||||||       ||  ||| |   | || |||  || | | ||  |    | || ||| || |  |  |          ||||||||||||||| || || ||||||||||||||||| ||| | ||||| ||||||||||| || |||||||||||||||||||| ||||| ||  | || ||||
cataatttgctttctgctaacatcagtcaaacagagaatgatgttgccacataatttgctttctgctaacaacg-agtgcatttctttccctgt----------cttgcagGTATTTGATTTGTTCGATACAAAACACAATGGTATTTTAGGATTCGAAGAATTTGCCCGTGCGCTCTCAGTATTTCATCCAAATGCACCTCTCGACGAGA

upper sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4

-----tgtccaatgaaaaatagtcaagtg-agatcctgtggatgcttacttt-ctttccagttagtatgacattgtattgctataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA
     | |    |||  |  ||| |  || | | | | |  ||      ||  | ||  | || ||||    ||||  || |       |||| | |||   || |||| |||||||| ||||||||||| ||||||||||| ||||  |||||||| ||||| || || ||||| || |||||||||||||| ||  | ||||| |
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtat----ttgtcctgttcatgattttgt-actgtc--tgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

upper sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 5

tgtccaatgaaaaatagtcaagtgagatcctgt--ggatgcttactttctttccagttagtatgacattgtattgctataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA-
|||  |  | |  ||    |  | | ||  |||    |   | | |  |  | ||  |  | |||        |  ||| | | |     |   |||   |||||||||| |||||||| ||||| ||||||||||| || || |||||||| |||||||| || ||||| || |||||||| ||||| ||  | ||||| | 
tgttta-cgtattatttcaacattatattttgttcaaaaattgattcacaattcaact--tgtgattggaatctaatatgaacttctctctaactctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTTCATCCAAATGCCCCTATTGATGATAA

upper sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4

--tgtccaatgaaaaatagtcaagtg--agatcctgtggatgcttactttctttccagttagtatgacattgtattgc-tataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA
  | ||   | |   ||  |  | |   | ||  |||  |    |   |||     | |   | ||   | ||||  | ||| | | || ||  |    |   |||||||||| |||||||| ||||||||||||||||| || || |||||||| |||||||| || ||||| || || ||||| ||||| ||| | ||||| |
tatatctgtttacgtatttttcaatattatattttgttcaaaaattgattcacattactccttgtggt-tggtatctcatatgaac-ttctctctaactt---agGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA

upper sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 4

----tgtccaatgaaaaatagtcaagtgagatcctgtggatgcttactttctttccagttagtatgacattgtattgctataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA
      ||  || |   |      |||   || |  |  |    |  | |    |     | | | |  ||||  || |       |||| | ||||  || |||| |||||||| ||||||||||| ||||| ||||| ||||  |||||||| ||||| || || ||||| || |||||||||||||| ||  | ||||| |
ttatgatctgattacttaagagttagttgtatgccatatacatatgatgtgaaccttagaatttttat-ttgtcctgttcatgattttgt-actgtt--tgtagGTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAGTTTGCACGAGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

upper sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5

tgtccaatgaaaaatagtcaagtgagatcctgtggatgcttactttctttccagttagtatgacatt-----gtattgctataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA
         ||   |  |    | | ||  |  |  | ||||    | ||   || |  || |  ||     | | ||||  ||    ||| ||| |  ||  |||| || || || ||||||||||| |||||||| || || || ||||| ||||||||||| || ||||| || ||||| || ||||| ||  | ||||| |
-------gtaatgtttctttcttcacattataagtgttcttaaacccatttttgtcaagatcaagtttagaagaaatgctgaaata--tgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA

upper sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 3

tgtccaatgaaaaatagtcaagtgagatcctgtggatgcttactttctttccagttagtatga-cattgtattgctataaccattgtcattgttc-----ttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA
      |||     |  | |  ||   |   ||      | | ||| ||   | | |||   |  |   |||| ||| ||    || |  | |||     ||| ||||||||||||| ||||| ||||| |||||||| || || |  |||||||| ||||| || || ||||| || |||||||||||||| ||| | || || |
------atgttccttcattagttggcttgtagtcttctttcagttttttcaaaatgagtccaaataaattattcctacaatttatgcctctattcaaatcttgtagGTATTTGACTTGTTTGACACAAAGCACAATGGAATACTAGATTTTGAAGAGTTTGCGCGTGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACA

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|5846848|gb|AI999931.1|AI999931

EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA

EST: gi|60354409|gb|DN221382.1|DN221382

EST:     AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA

EST: gi|6194508|gb|AW146612.1|AW146612

EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA

EST: gi|211071789|gb|FK958795.1|FK958795

EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA

EST: gi|9952360|gb|BE638943.1|BE638943

EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA

EST: gi|211483288|gb|FL326631.1|FL326631

EST:     TGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: TGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA

EST: gi|211071790|gb|FK958796.1|FK958796

EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA

EST: gi|5325037|gb|AI783228.1|AI783228

EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 89

GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 124

GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 116

GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tctttccagttagtatgacattgtattgctataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA

                            ctataac  putative branch site (score: 116)
                                           ttgttctt  putative PPT
                   attgtatt  TA-rich tract

Data associated with selected splice site

Sequence

Basic information

Orthologous splice sites

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

RNA-Seq data