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

gtgtgatatcatctaactagtttcattggccacttgtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC

Basic information

species	Zea mays
transcript	GRMZM2G009030_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 3

gtgtgatatcatctaactagtttcattggccacttgtttgat------tgctctcttgtttttt---actttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC
|| ||   ||||||     |||| |||  |||| | ||  ||        |  | || ||||||   ||||  |||  |    ||  |||||| ||||||| |||||||| ||||||||||| ||||| ||||| |||||||||||||| | ||||||  ||||||||||||||||||||||||||||||| ||| |||
gtctgcagtcatctt----gttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGAAGCTATGACTTAAACTTTAAGAATCAGCCTAATGATGGAGCTCATGTTC

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 4

gtgtgatatcatctaactagtttcattggccacttgtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC
||| |  |   | | | || ||   |||   |    |||||    || |||||  |    | |  |  | ||| ||||    |  ||||||| ||||| |||||||||||||| || || |||||    || ||||||||||| |||||| | ||||| ||||| ||||| ||||||||||| ||| |||
gtgggtgaagctttgattatttctgttgcata---atttgaaaattcacttgtgct--gatctggaaataaaaaacaa----tggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 4

gtgtgatatcatctaactagtttcattggccacttgtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC
  ||||     | | | || ||   |||   ||||   ||| |  || |||||  |   ||  ||||   ||| | ||||     ||||||| ||||| |||||||||||||| || || |||||    || ||||||||||| |||||| | ||||| ||||| ||||| ||||||||||| ||| |||
--gtgaagc--tttgattatttctgttgcatactt---tgaatattcacttgtgctgatctggaaat---aaaaaaaaat---ggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 2

gtgtgatatcatctaactagtttcattggccacttgtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC
||| |  |   | | | || ||   |||   |    ||||| |  || |||||  |    | |  |  | ||| ||||    |  ||||||| |||||||||||||||||||| || || |||||    || ||||||||||| |||||| | ||||| | ||| ||||| ||||||||||| ||| |||
gtgggtgaagttttgattatttctgttgcata---atttgaatattcacttgtgct--gatctggaaataaaaaacaa----tggtgcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC

upper sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3

gtgtgatatcatctaactagtttcattggccacttgtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC
        |   |    |  |    ||     ||| |    ||    | |  ||     ||||||    |  | | ||||    |||||||||||||| || ||||||||||| || || |||||| | || || |||||||| |||||| | || |||||||| || || ||||||||||| ||  |||
-------gtaggcgggttgttgcttttcttttcttttgcagtttgattttccttgcagcctttaaggactccaaataaat---gatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC

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|6095531|gb|AW120198.1|AW120198

EST:     TTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAA                         ATCAAAATTGG-ATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG
genomic: TTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAAgtgtgatatc ... cctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG

EST: gi|67024736|gb|CO453485.1|CO453485

EST:     GTCTTATTTTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAA                         ATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG
genomic: GTCTTATCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAAgtgtgatatc ... cctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG

EST: gi|116828215|gb|EC855677.1|EC855677

EST:     GGCAGGCTACACTGGAAAA                         ATC-AAATTGGTATNGATGTTGCGGCATCTGAG-TCCTTACAAAGGATGGG
genomic: GGCAGGCTACACTGGAAAAgtgtgatatc ... cctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG

EST: gi|76290528|gb|DV030096.1|DV030096

EST:     AGGCAGGCTACACTGGAAAA                         ATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG
genomic: AGGCAGGCTACACTGGAAAAgtgtgatatc ... cctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG

EST: gi|76011517|gb|DT938687.1|DT938687

EST:     GTCTTATCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAA                         ATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG
genomic: GTCTTATCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAAgtgtgatatc ... cctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG

EST: gi|6020507|gb|AW065435.1|AW065435

EST:     GTCTTATTTTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAA                         ATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG
genomic: GTCTTATCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAAgtgtgatatc ... cctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGG

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), 46 (downstream exon)
Score: 81

TGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAGAGAGGGTCTTATCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAAgtgtgatatc ... cctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 88

Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 131

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 511

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC

                                            tcctaat  putative branch site (score: 511)
                 ttttttactttaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgatatcatctaactagtttcattggccacttgtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA