ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTAAAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcacgagcccttctacactttgttaatatcctagatccattttttttggattgctgttcagatttagtgacccgatttctcgctgcag

Basic information

species	Zea mays
transcript	GRMZM2G120115_T02
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 6

TGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTAAAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcacgagcccttctacactttgttaatatcctagatc--cattttttttggattgctgttcagatttagtgacccgatttctcgctgcag
|||||||||  ||||||| |||||||||||| |||||||| | || || ||||| || || || || ||||| || ||||||||||||||||||||||||||| ||| | ||  ||||   ||||   |||||||  |  |    || |   ||     ||     ||   || |   | | ||||   | |||||
TGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAAAAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtactttta-gactcctttagcactc-attaatatatttcactggcactcacttcaacatgtgaaacattgttcgattctc-attttatgttgcag

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|71444906|gb|DR825956.1|DR825956

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

EST: gi|71310156|gb|DR791369.1|DR791369

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

EST: gi|211365944|gb|FL391110.1|FL391110

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

EST: gi|76290013|gb|DV029581.1|DV029581

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATTTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

EST: gi|60394595|gb|DN227465.1|DN227465

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

EST: gi|78108843|gb|DV527260.1|DV527260

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

EST: gi|37392993|gb|CF633751.1|CF633751

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

EST: gi|88749057|gb|DY533198.1|DY533198

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATTTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

EST: gi|84977510|gb|DW475932.1|DW475932

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

EST: gi|6952519|gb|AW424587.1|AW424587

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGCTACTGGCTATCTTC
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTC

EST: gi|50328759|gb|CO523885.1|CO523885

EST:     AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATA

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), 48 (downstream exon)
Score: 134

TGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTAAAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcac ... ctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCATAAAAGCTTGGAAGGCAGCTGAGGTTCCAATGATCGA

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 218

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 175

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 260

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTAAAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCTGgtagtttcacgagcccttctacactttgttaatatcctagatccattttttttggattgctgttcagatttagtgacccgatttctcgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT