ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagcgaccgcgccgcactccattgctgctttctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG

Basic information

species	Zea mays
transcript	GRMZM5G868433_T04
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G868433_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 1

gtaagcgaccg-cgccgcactccattgctgcttt-ctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG
||||| |  || |||||    ||||||| ||  | |||   ||  | |||   |||  |  |  | |         |||  ||||| || || |      |  | | ||||| ||||||||||||  ||||||| |||||||||||| || ||||||||| ||||||| ||||||  |||||| |||| ||  ||||||||| || | |
gtaagagctcgtcgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtcccgatctgaccctggtg-ggtttcgctgttc------gctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG

upper sequence: GRMZM5G868433_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 1

gtaagcgaccgcgccgcactccattgctgctttctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTG---CCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG
                           |    || |    |   || |  | |      || ||  |  ||   | | |   |  || |||   ||| || ||| ||||| || | |||| || ||||| |||||||   ||||||||||| ||    ||||||||||| |||||||||||||| || || | |||||||||| | |   
--------------------------gtaagctcccgaaccctagctcgatccagcgactg-ctcggccgtgcggatct--ctgagcggtgtgtgtgtgt-gtgcagATGGCGGCGGAGGTGGCGAAGGCGGCGGTGGTGCCGGAGTCGGTGCTGAAGAAGCGGAAGCGGGAGGAGCAGTGGGCGGCGGACAGGAAGGAGAAGGCGC---

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|211173109|gb|FK956294.1|FK956294

EST:     TCTCCTACGCAGATCGTCCAGGTAAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTG-CGGAGTCGGTACTCCGCAAG
genomic: TCTCCTACGCAGATCGTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG

EST: gi|94477419|gb|EB706377.1|EB706377

EST:     CCCCTCTCCTACGCAGATCGTCCAGGTAAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: CCCCTCTCCTACGCAGATCGTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG

EST: gi|211173107|gb|FK956292.1|FK956292

EST:     TCTCCTACGCAGATCGTCCAGGTAAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: TCTCCTACGCAGATCGTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG

EST: gi|211171435|gb|FK956283.1|FK956283

EST:     TCTCCTACGCAGATCGTCCAGGTAAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: TCTCCTACGCAGATCGTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG

EST: gi|211171436|gb|FK956284.1|FK956284

EST:     GTCCAGGTAAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: GTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG

EST: gi|211171440|gb|FK956288.1|FK956288

EST:     TCTCCTACGCAGATCGTCCAGGTAAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: TCTCCTACGCAGATCGTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG

EST: gi|211173115|gb|FK956300.1|FK956300

EST:     TCTCCTACGCAGATCGTCCAGGTAAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: TCTCCTACGCAGATCGTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG

EST: gi|211173112|gb|FK956297.1|FK956297

EST:     CTCCTACGCAGATCGTCCAGGTAAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: CTCCTACGCAGATCGTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG

EST: gi|211173121|gb|FK956306.1|FK956306

EST:     TCTCCTACGCAGATCGTCCAGGTAAG                         ATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG
genomic: TCTCCTACGCAGATCGTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAG

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: 837

ACATAACCCGCCATTCCCACTCCCCTCGCCGCCTGCGTCCACCTCCGCCCCCCGCCCTCCCCGCGTCCCCCCTCTCCTACGCAGATCGTCCAGGTAAGgtaagcgacc ... ggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1055

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 858

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 409

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgaccgcgccgcactccattgctgctttctctgttcgctgcgcatttcgatctttggctaagaagttgcggtttggtttggccgtgctcgtgggtcgtgtagATGTCGTCCGAGGCGGTGAAGGTGGCGGTGCCGGAGTCGGTACTCCGCAAGCGGAAGCGCGAGGAGCAGTGGGCCGCCGAGAAGAAGGAGAAGTCCCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT