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

...gcatgcactcggctgtaccaccacccaagcaaaagcgccgctgcttgctagctagtgctcggtgatgacagctgaacagcgactgctttcccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGCGACAACTTCTACGAGAACGGCCTGACGGGCACGGATGACGAGGCGTTCG

Basic information

species	Zea mays
transcript	GRMZM2G152477_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152477_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g13540.1 (Oryza sativa), 3'ss of exon 1

-----gcatgcactcggctgtaccaccacccaagcaaaagcgccgctgcttgctagctagtgctcggtgatgacagctgaacagcgactgctttcccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGCGACAACTTCTACGAGAACGGCCTGACGGGCACGGATGACGAGGCGTTCG
     | ||  | |    || |          |  |     |    |  ||  ||  |||         |  | |  | |  |  |||   ||  |    || ||||||| | |||||||||| |||| |  || |||||||||||||||||||| ||||| ||||||||| | || || || |||   |||||| ||||||| |
tatttgtat-tattaaagtgaatactttttttaaaactgaaggtattattttttaaatagcaaagacaaacaata-ttaagtatggacaatttatc---atgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGTGACAATTTCTACGAGGATGGACTCACTGGCGTCGATGACCAGGCGTTTG

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|211072232|gb|FL200232.1|FL200232

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|71309437|gb|DR791006.1|DR791006

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGGCAGGGTTGGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCG
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGG-CAGGGTTGGGG-AGCAGCTCAGCATCGACTTCGTCATATCCACCG

EST: gi|211072234|gb|FL200234.1|FL200234

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|211072233|gb|FL200233.1|FL200233

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|20299974|gb|BQ162917.1|BQ162917

EST:     GACTGGGGCCCAAAAGGGCCGCGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GACTGGGG-CCGAAAGGG-CACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|74245680|gb|DT653594.1|DT653594

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|148966046|gb|EE016980.2|EE016980

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|78118175|gb|DV536562.1|DV536562

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|149014532|gb|EE044166.2|EE044166

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|149008292|gb|EE040441.2|EE040441

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|37417545|gb|CF646426.1|CF646426

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAG
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAG

EST: gi|211074959|gb|FL200236.1|FL200236

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

EST: gi|71430081|gb|DR811131.1|DR811131

EST:     GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAG                         ATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC
genomic: GCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGC

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), 48 (downstream exon)
Score: 132

GCTGGAGCACCCGCCCAAGGACGGCGGCTCGCTCAGCCTGCTCGTCGTCGGCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaacc ... ccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGCGACAACTTCTACGAGAACGGCCTGACGGGCACGGATGACGAGGCGTTCG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 392

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgctagctagtgctcggtgatgacagctgaacagcgactgctttcccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGCGACAACTTCTACGAGAACGGCCTGACGGGCACGGATGACGAGGCGTTCG

                                     ctgctttccc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgcactcggctgtaccaccacccaagcaaaagcgccgctgcttgctagctagtgctcggtgatgacagctgaacagcgactgctttcccatgtgtagATGGGCAGGGTTGGGGAGCAGCTCAGCATCGACTTCGTCATATCCACCGGCGACAACTTCTACGAGAACGGCCTGACGGGCACGGATGACGAGGCGTTCG

gcatgca
- - - - - -gctgtac
- - - - - - - - - caccacc
- - - - - - - - - - - - -caagcaa
- - - - - - - - - - - - - - - - - - - -gctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - gctagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acagctg