ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AAGATCATAATCACTTTCCGTTTAGCAATCTGCTTCCAAATATATGGCCAGGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaatcaataatactgctcggtgtcatgcacaaatgcatgcactatgtgtatgcatttagttggtagcgggcgaaacatgttaataatacaagc...

Basic information

species	Zea mays
transcript	GRMZM2G097959_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G097959_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g12550.1 (Oryza sativa), 5'ss of exon 8

AAGATCATAATCACTTTCCGTTTAGCAATCTGCTTCCAAATATATGGCCAGGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgtt-------gaatcaataatactgctcggtgtcatgcaca-aatgcatgcactatgtgtatgcatttagttggtagcgggcgaaacatgttaataatacaagc
| |  ||   |||||| || |||||||| |||||||| |||||||||||||| ||||| ||||  |||||| ||||||  || ||||     || || |||| ||||          |      | |  || | |||||||||||  | |  | |||| | || ||    ||  |    |   | |  ||  | ||  |  |      
ATGGCCAATCTCACTTCCCATTTAGCAACCTGCTTCCTAATATATGGCCAGGTCATGATAGAAGTTTCAAAGCACAAGGAAGAGACAGAGCATTCAGAAGgtctgttcttcctcatctttcccttccctcttgctgtcatgcacatgaagtgtacactctatgaatcatgtttctatacaatagcctcaa--ttttggtttt------

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|32841617|gb|CD981298.1|CD981298

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|74244282|gb|DT652196.1|DT652196

EST:     CAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: CAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|76011046|gb|DT938216.1|DT938216

EST:     CAGAAAGTTCAAATCCCAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: CAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|32841400|gb|CD981081.1|CD981081

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|32841273|gb|CD980954.1|CD980954

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|32839529|gb|CD979210.1|CD979210

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|31356757|gb|CD441114.1|CD441114

EST:     GGCATGACAGAAAG-TCAAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGCATGACAGAAAGTTC-AAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|32841038|gb|CD980719.1|CD980719

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGTCAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|32841023|gb|CD980704.1|CD980704

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|93012401|gb|EB637921.1|EB637921

EST:     CAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: CAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|32840905|gb|CD980586.1|CD980586

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|32841064|gb|CD980745.1|CD980745

EST:     ATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: ATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|33092415|gb|CF052409.1|CF052409

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|32841405|gb|CD981086.1|CD981086

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|32841667|gb|CD981348.1|CD981348

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

EST: gi|31356903|gb|CD441260.1|CD441260

EST:     GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAG                         ATATGATGCCGACGTGAAGAGTAAGTTACAAGCAACCCCTCTTCTTCCGAA
genomic: GGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAA

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: 43 (upstream exon), 36 (downstream exon)
Score: 23

AAGATCATAATCACTTTCCGTTTAGCAATCTGCTTCCAAATATATGGCCAGGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaa ... ttggtaccagATATGATGCCGACGTGAAGAGTAAGTTACAAGCAAACCCTCTTCTTCCGAAAATCACCATGGTTGGCATCTCAATGGGTGATGGTGCACAGATGAGCAAA

Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 13

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 15

Block sizes: 47 (upstream exon), 37 (downstream exon)
Score: 13

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATCATAATCACTTTCCGTTTAGCAATCTGCTTCCAAATATATGGCCAGGGCATGACAGAAAGTTCAAATCACAAGAGAGTGACAATAAGTTTAGCAGgtttgttgaatcaataatactgctcggtgtcatgcacaaatgcatgcactatgtgtatgcatttagttggtagcgggcgaaacatgttaataatacaagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA