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

gtaaggagtcattccctcgtccaatggcaagaatatacagaaatatcagcacacgagtaacactttgcctgtggacgttgtcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTAC

Basic information

species	Zea mays
transcript	GRMZM2G077669_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6

gtaaggagtcattccctcgtccaatggcaagaatata-cagaaatatcagcacacgagtaacactttgcctgtg--gac--gtt----gtcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTAC
|||||    |    | |  |      |||  |   || | || || ||    | |  ||  |  | |    ||   |||  |||    ||  | || |||| || |||||||||||||| |||||||| || ||||| || |||||||||||  | |||    || | || || ||||| ||| |  |    ||   ||
gtaagtccccccaacattctttttctgcaccatagtagctgagatttcgtgtcccatgtctctgtgttgtggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC

upper sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6

---------gtaaggagtcattccctcgtccaatggcaagaatatacagaaatatcagcacacgagtaacactttgcctgtggacgttgt-cttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTAC
         | |   || |  |     | |   |          |        |||    |    ||  |    |   |||    | | |  ||||| |||| || |||||||| |||||||||||||| || ||||| || || ||||||||  ||||| | |||||||| || ||||| |||||  |  | ||     
ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT

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|50336618|gb|CO531744.1|CO531744

EST:     ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCACTGTCATGTTCGGGAAGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC

EST: gi|24769648|gb|CA404777.1|CA404777

EST:     ATTTCTTCCGCATCCCTCTCAACTTATTTGTTTGTGTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC

EST: gi|91872557|gb|EB402514.1|EB402514

EST:     ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC

EST: gi|60344176|gb|DN211149.1|DN211149

EST:     ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC

EST: gi|149030376|gb|EE154822.2|EE154822

EST:     ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC

EST: gi|149009313|gb|EE153898.2|EE153898

EST:     ATTTTTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTTTATTTTCCTT
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC

EST: gi|18964118|gb|BM660820.1|BM660820

EST:     ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTG-GTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC

EST: gi|211446928|gb|FL456344.1|FL456344

EST:     ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCNACTGTCATGTTCGGGATGTGTTCTATCTTCCT
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATC-ACTGTCATGTTCGGGATGTGTTCTATCTTCCT

EST: gi|211399039|gb|FL440973.1|FL440973

EST:     ATTTCTTCCGCATCCCTCTCAACTTATTTGTTTGTGTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC

EST: gi|91872556|gb|EB402513.1|EB402513

EST:     ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAAT                         GTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTTTATTTTCCTT
genomic: ATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTC

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), 49 (downstream exon)
Score: 55

GAAGATGAGGTCTCAGTACATTCCTGAGGAAGCAAGAAGCACAATCATGAATTTCTTCCGCATCCCGCTCAACTTATTTGTTTGTGTGGTGCTTTACAATgtaaggagtc ... tcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTAC

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 94

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 195

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tacagaaatatcagcacacgagtaacactttgcctgtggacgttgtcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTAC

                   gagtaac  putative branch site (score: 133)
                                          ttgtctttt  putative PPT
     aaatatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggagtcattccctcgtccaatggcaagaatatacagaaatatcagcacacgagtaacactttgcctgtggacgttgtcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTAC

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