ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG

Basic information

species	Zea mays
transcript	GRMZM2G079538_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 9

acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgat----ttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
   || |   ||   |   |   | | | | |   |     ||| |||    | | |  ||| ||  | || || |  || | | | |      ||  ||||||||| |||||||||||||| || ||||||||||| ||||| |||||||| ||||| ||||| ||||||||||| ||||| ||||||||||||
---tagaatcttgcatggcgtactactaattcttcctagaaaagcttggctagatatgcttttct-gttttgtccccttaccctgttaagacaatacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG

upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA02G46200.1 (Glycine max), 3'ss of exon 11

------acttaaataattatct--tttgccatgccattacg-atcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
         |   |  || |    |   | |  |  ||| | || |  | ||  |     |  |||||| ||     ||||| ||| |    |     | || ||  ||||| |||||||||||||| |||||||||||||| ||||  |||||   ||||||||| || |||||||| ||||||||| |||||||||| 
agatttttcttggtctttgtgagatcaacaaacctgttatgcattctctcaaattcactattatgtattctctcc--cttattgctctgctct-----taatgat--agGACTAATTTGATGAAGCTCCGTTCTGATTATAAGGATGCTTTTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTCAAA

upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA14G02530.2 (Glycine max), 3'ss of exon 11

-acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
   |||| |    ||  ||     ||   || |  ||   |     |  ||||||  || | |  | ||  | |  ||   |  | || | |       ||||| |||||||||||||| |||||||||||||| ||||  |||||   ||||||||| || |||||||| ||||||||| ||||||| || 
tgtttaattgccaattcttgatgttgtgtttcctgtcatgtccttat-atagtggattactattgtcattctcttccttattggtctgctcttaatgatagGACTAATTTGATGAAGCTCCGTTCTGATTATAAGGATGCTTTTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAA

upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 6

----acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
       || ||| | |  ||     | ||  ||  |    ||   |||   |  |||||  ||||   | | || | |||||  |||     ||||  ||||||||||||||||||||||||||||||||||||||||||| |||| |   |||||||||||| || ||  |  |||||||  | ||||| |||
tcatcaatatatattgaaattgcctgacgcattttagcatgctatcaggcacttctggtgatttttgtctgtttt-ttgctgtg-cttgctgcttat--tgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG

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|211104575|gb|FL031921.1|FL031921

EST:     ACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|211169880|gb|FL077609.1|FL077609

EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|32830086|gb|CD969764.1|CD969764

EST:     ACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|13558100|gb|BG549456.1|BG549456

EST:     ATTCTCAGAACACCTTTGCAATGTTGTGTTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ATTCTCAGAACACCTTTGCAATGCTGAG-TACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|32942914|gb|CF047733.1|CF047733

EST:     GAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|60358853|gb|DN225826.1|DN225826

EST:     GTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|6227238|gb|AW155837.1|AW155837

EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|32829046|gb|CD968724.1|CD968724

EST:     ACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|32828877|gb|CD968555.1|CD968555

EST:     ACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|211169873|gb|FL077602.1|FL077602

EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|7145229|gb|AW506710.1|AW506710

EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|13558537|gb|BG549893.1|BG549893

EST:     ATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGTTGTTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAA
genomic: ATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAG-TTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAA

EST: gi|32867030|gb|CF006712.1|CF006712

EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|67019048|gb|CO447797.1|CO447797

EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

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), 47 (downstream exon)
Score: 207

GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 324

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG