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

...tgtgcactaatgattcaatttgtttgttttaccaaaaacttgtttgatttttcatctcctgttatcttgaatgctctcttgttttgctatcctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG

Basic information

species	Zea mays
transcript	GRMZM2G158147_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 3

------tgtgcactaatgattcaatt-tgtttgttttaccaaaaacttgtttgatttttcatctcctgtta---tcttgaatgctctcttgttttg----ctatcctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG
        |||||  |  |  || |    |||  |  |  |  |  |  |||||     ||| |  |   |   | |||     || ||     |     ||||   ||  ||||||||||| ||||||||||| || ||| ||||||| || |||||||||||||| ||| ||||||||||||||||||| |||||||||
gtatttgatgcacagaaaaagcattagcatttaatgaattatcatttgttttgaggaaacatgtaataccagatttttgttctttccctaaaaataaatactatttgctc-cagGTAGCAGCATATGATACAGTGGCGAAGAAGATGGCGTTCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAG

upper sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g02050.2 (Oryza sativa), 3'ss of exon 3

------tgtgcactaatgattcaatt-tgtttgttttaccaaaaacttgtttgatttttcatctcctgtta---tcttgaatgctctcttgtttt----gctatcctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG-------------
        |||||  |  |  || |    |||  |  |  |  |  |  |||||     ||| |  |   |   | |||     || ||     |     ||||   ||  ||||||||||| ||||||||||| || ||| ||||||| || |||||||||||||| ||| ||||||||||||||||||| |||||||||             
gtatttgatgcacagaaaaagcattagcatttaatgaattatcatttgttttgaggaaacatgtaataccagatttttgttctttccctaaaaataaatactatttgctc-cagGTAGCAGCATATGATACAGTGGCGAAGAAGATGGCGTTCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAGGTACAGATAAATT

upper sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 3

tgtgcactaatgattcaatt--tgtttgttttaccaaaaacttg--tttgatttttcatctcctgttatc--ttgaatgctctcttgttttgctatcctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG
     |    |  ||| |||  ||||   || |  |   || |   ||| ||| | | | |||||  ||   |  | |  |||  |   ||  ||| || |  ||||| ||||| ||||| ||||| | |||| |||||||||||||||||||||||||   | | |||||||| ||||| || |||||||||
-----aaggttccttccattattgttaacttgaagacgcacatcatttttattatgcttttcctgcaatgaatccattaatcttctaacttattatactat-gcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCACGTGCTAAGGATTTTCTCTTCATTTCAGGAACCAAG

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|60338703|gb|DN205676.1|DN205676

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAA

EST: gi|211399264|gb|FL448232.1|FL448232

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32830226|gb|CD969904.1|CD969904

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32828661|gb|CD968339.1|CD968339

EST:     TCCTGAGCATGGCTGGTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|78180099|gb|DV550472.1|DV550472

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32829799|gb|CD969477.1|CD969477

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32829244|gb|CD968922.1|CD968922

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32828636|gb|CD968314.1|CD968314

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32830289|gb|CD969967.1|CD969967

EST:     CTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: CTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|60346069|gb|DN213042.1|DN213042

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32830236|gb|CD969914.1|CD969914

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|60357884|gb|DN224857.1|DN224857

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32829367|gb|CD969045.1|CD969045

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|148942989|gb|EC888037.2|EC888037

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

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), 43 (downstream exon)
Score: 38

ACATCCAACAGAAAAGAGGGACTTGTACAACCCAGATCACGGGAAGAAGGTCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 87

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

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 40

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gatttttcatctcctgttatcttgaatgctctcttgttttgctatcctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG

 gtttgat  putative branch site (score: 40)
                            ctctcttgttttgcta  putative PPT
                ttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgcactaatgattcaatttgtttgttttaccaaaaacttgtttgatttttcatctcctgttatcttgaatgctctcttgttttgctatcctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG

- tgcacta
- - - - - tgattca
- - - - - - - - - -ttgtttg
- - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - accaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgct