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

gtttgatactgtggacttgatacagtgcatggcaaactaagatcaatatggtgattacatcttgaattagttgtgttcgtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTTATATTGAACTCGTACTCCCTGACCTCATTTGATCTCCTCTTGGACTCGG

Basic information

species	Zea mays
transcript	GRMZM2G180889_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G180889_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g20420.2 (Oryza sativa), 3'ss of exon 16

----gtttgatactgtg----gacttgatacagtgcatggcaa-actaagatcaatatggtgattacatc---ttgaattagttgtgttcgtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTTATATTGAACTCGTACTCCCTGACCTCATTTGATCTCCTCTTGGACTCGG
     || |  ||| |        ||| ||  ||  |       |  ||  | || | |   ||    ||    | ||    | ||||       || ||||||||||||||||||| || ||||||||||||||| || | |||||||| ||  || |  | |||||||| ||||| |||||||||||| ||||| |  
ctttattggcaactttaccaaattttggtaaggttgaaaatggcatcaaagtgaacaggcccatagtgtcggtcttaaactttggtgtgaaatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTCATTGTGGATCCATACTCCCTCACCTCGTTTGATCTCCTCCTGGACACCA

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|32840433|gb|CD980114.1|CD980114

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTTCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|211495745|gb|FL475524.1|FL475524

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|40335824|gb|CK369894.1|CK369894

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|26558128|gb|CA830363.1|CA830363

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTTCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|37387566|gb|CF630980.1|CF630980

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCTGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|211495744|gb|FL475523.1|FL475523

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAACCAAATCGGCGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|21987659|gb|BQ779187.1|BQ779187

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTTCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|87155463|gb|DY400252.1|DY400252

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTTCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|32842248|gb|CD981929.1|CD981929

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTTCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|32842540|gb|CD982221.1|CD982221

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTTCACCAGCCCGACAAG                         GTGGTGCTGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|32842247|gb|CD981928.1|CD981928

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTTCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCCAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

EST: gi|32841989|gb|CD981670.1|CD981670

EST:     TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTTCAACAGCCCGACAAG                         GTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT
genomic: TCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTT

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: 46 (upstream exon), 44 (downstream exon)
Score: 15

AACTGGGTTGGAAACTGATATTCAGACATTTGGATCCATAAAGACGGTTCTCACGTCGGGTTGGCTGCGGGATGAGAACTCCTTCCAACAGCCCGACAAGgtttgatact ... gtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTTATATTGAACTCGTACTCCCTGACCTCATTTGATCTCCTCTTGGACTCGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 383

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 284

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaactaagatcaatatggtgattacatcttgaattagttgtgttcgtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTTATATTGAACTCGTACTCCCTGACCTCATTTGATCTCCTCTTGGACTCGG

        atcaatat  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatactgtggacttgatacagtgcatggcaaactaagatcaatatggtgattacatcttgaattagttgtgttcgtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTTATATTGAACTCGTACTCCCTGACCTCATTTGATCTCCTCTTGGACTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC