ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgagtaccagtcaggaattgctactcgtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTGCTCTTTCTCTCATCATAGGCTTTGGTTTGTTTAGGGTGGGGCTCCTTCC

Basic information

species	Zea mays
transcript	GRMZM2G029685_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G029685_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G04920.1 (Arabidopsis thaliana), 3'ss of exon 4

--gtgagtaccagtcaggaat--tgcta-ctcgtattccc-attgttctggtacatttcaattatgtttgctgcacaattttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAG-GAAGTTACTTGCCTTGCTCTTTCTCTCATCATAGGCTTTGGTTTGTTTAGGGTGGGGCTCCTTCC
   ||  |||  ||      |  ||||| ||  | ||    |||||    |||   || ||  || | |  ||  |||| ||| ||||||||||||||| |||||||||||||||| ||     ||||  |    | ||    | |   |  |  |   |  |  |   |      |   | |  ||  
gtatgtatactggttttccctcttgctatcttctgtttttgattgtgactgta-gctttaagaatctgttttgatcaatgttt-gcagACAAAGGCTGGTGATGCCAAGAAGAAGTGAGATCCTGAAGAGAGAATCTTTATCTTGTGGGTTCTTGTTCTCCATAATCAATCACCTTTTATGTTATTTG-

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|5761771|gb|AI966819.1|AI966819

EST:     GAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: GAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|211014258|gb|FL283800.1|FL283800

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAATTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|15079941|gb|BI388886.1|BI388886

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAATTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|211014266|gb|FL283808.1|FL283808

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAA
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAA

EST: gi|113701166|gb|EE678670.1|EE678670

EST:     AAGAACAGGGCGAAGAAAATCCGTGGTTTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|16926632|gb|BM079700.1|BM079700

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|37376305|gb|CF624665.1|CF624665

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|60397441|gb|DN230257.1|DN230257

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|60355885|gb|DN222858.1|DN222858

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

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), 49 (downstream exon)
Score: 99

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTGCTCTTTCTCTCATCATAGGCTTTGGTTTGTTTAGGGTGGGGCTCCTTCC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 131

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 79

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 71

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTGCTCTTTCTCTCATCATAGGCTTTGGTTTGTTTAGGGTGGGGCTCCTTCC