ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttggaatgtccacttcactgattggtcatgttgttcatttcttgatactttactatcactgacctgcagactgtgacaagcttaacccaatgac...

Basic information

species	Zea mays
transcript	GRMZM2G075101_T03
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G075101_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g64920.1 (Oryza sativa), 5'ss of exon 8

GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttggaatgtccacttcactgattggtcatgttgttcatttcttgatactttactatcactgacctgcagactgtgacaagcttaacccaatgac-
||||| ||||||||||| || |||||||| || || ||||||||||| || |||||||||||||||||| | |||||||||||||| || ||||| |||||| |   ||||| |    || | |      |  ||||| |||||||  | |    | |  ||  ||  |         |||   | |||    |||    
GAAATTCATCCTTGGACACATATGATGGAGGTCCCTCAATTGCATGGTTTTGGTCCAGCTGCTAATCGCTTGTTGGAGGCATATAACACACTTTTGAAGgtactagcggaatatttggtttatttgacattt-tgttgctcatttcaagttttgcttccctctatggtcaatgtgtcatgatctggttatttgaattggt

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|93012884|gb|EB638404.1|EB638404

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|37398489|gb|CF636559.1|CF636559

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|74246322|gb|DT654236.1|DT654236

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|71761514|gb|DR959451.1|DR959451

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|32942644|gb|CF047463.1|CF047463

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|6601609|gb|AW256155.1|AW256155

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACCCTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|71773508|gb|DR971408.1|DR971408

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|76020456|gb|DT947626.1|DT947626

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|37388177|gb|CF631295.1|CF631295

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|31364678|gb|CD449033.1|CD449033

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|89250411|gb|DY622197.1|DY622197

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

EST: gi|32942426|gb|CF047245.1|CF047245

EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

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: 103

GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCTGGTTCACTGTCGGCTTCTAATGAGCCTTCATCTGTGACCAAGATTATTT

Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 25

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 22

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 70

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttggaatgtccacttcactgattggtcatgttgttcatttcttgatactttactatcactgacctgcagactgtgacaagcttaacccaatgac

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG