ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GAAGCCGCGGGAGGAGTCCCCTATCGGCGCCAACGAGATCCGCATCACGGCGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttcggtcgacggctactctctgctacttccttgctcgtttgttcccgccggccgccgccgttcggcctgtccatctatacgtagaaggaaagc...

Basic information

species	Zea mays
transcript	GRMZM2G142111_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G142111_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g34940.1 (Oryza sativa), 5'ss of exon 1

GAAGCCGCGGGAGGAGTCCCCTATCGGCGCCAACGAGATCCGCATCACGGCGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttcggtcgacggctactctctgctacttccttgctcgtttgttcccgccggccgccgccgttcggcctgtccatctatac-gtagaaggaaagc
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GAAGCCGCGGGAGGAGGCGGCCATCGGCGCCAACGAGATCCGCATCACCGCGCAGGGCCGCACCCGCAACTACATCACCTACGCCCTCGCCCTGCTCCAGgtccgccttcctcctcctccgccttcgatttgttttgttttttgttttttttt-tgggtggggagagctagggtttagtgcgggttcagtaatctcgccgc

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|78122944|gb|DV541328.1|DV541328

EST:     CGCGGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAG                         GACAATGCAACAGATGACATTGTCATCAGGGCCGTGGGAGGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|91874466|gb|EB404423.1|EB404423

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|71435668|gb|DR816718.1|DR816718

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|211038564|gb|FL344525.1|FL344525

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGGTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|83278985|gb|DV942993.1|DV942993

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|211006797|gb|FL317956.1|FL317956

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGGTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGTATGGGCGATCAA
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAA-GGGCGATCAA

EST: gi|211470848|gb|FL358523.1|FL358523

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGGTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|211116607|gb|FL350319.1|FL350319

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGGTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|211312453|gb|FL348221.1|FL348221

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGGTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|211401785|gb|FL336222.1|FL336222

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGGTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|32790682|gb|CD942918.1|CD942918

EST:     GCAGGGCCGGCCCCGCAACTACATCACCTATGGCGCTCGCCCTGCTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: GCAGGGCCGGCCCCGCAACTACATCACCTAT-GCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|211442302|gb|FL322986.1|FL322986

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGGTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

EST: gi|211442303|gb|FL322987.1|FL322987

EST:     CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGGTCCAG                         GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC
genomic: CGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAAC

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: 158

GAAGCCGCGGGAGGAGTCCCCTATCGGCGCCAACGAGATCCGCATCACGGCGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttc ... tccattacagGACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCCGCGGGAGGAGTCCCCTATCGGCGCCAACGAGATCCGCATCACGGCGCAGGGCCGGCCCCGCAACTACATCACCTATGCGCTCGCCCTGCTCCAGgttcgggttcggtcgacggctactctctgctacttccttgctcgtttgttcccgccggccgccgccgttcggcctgtccatctatacgtagaaggaaagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaggaaa