ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGACAACTCGATGGAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagctttaaatccttttttctatttgttaagtgaaatctaggcactatacttgtcctgtgatcctgactgtcaaatctacatgcaatttgtggaatttag

Basic information

species	Zea mays
transcript	GRMZM2G365160_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G365160_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g42960.2 (Oryza sativa), 5'ss of exon 2

TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGACAACTCGATGGAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagctttaaatccttttttctatttgttaagtgaaatctaggcactatac---ttgtcctgtg-atcctgac-tgtcaaatctacatgcaatttgtggaatttag
 || || ||||||||| | |||||||||||||||||||| || ||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||| || | |   ||||  ||   |||| ||||||||       | |      || | |||| ||  |||| | |||||   ||||  |   |||| ||| |||
CTGCTCAGCCCACATGCTATGGGTTGGTGAGCGCACTCGCCAGCTCGATGGAGCTCATGTTGAATTTCTCCGTGGTGTTGCCAACCCTCTTGGCATAAAGgtcagcattgagtttattttcataaa-gttatgtgaaatcctaatgttgtttgcagtgccttgtggatgttgacatttcaaactgacattgaccctgtgtaatgtag

upper sequence: GRMZM2G365160_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ08096 (Selaginella moellendorffii), 5'ss of exon 3

TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGACAACTCGATGGAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta---aatccttttttctatttgttaagtgaaatctaggcactatacttgtcctgtgatcctgactgtcaaatctacatgcaatttgtggaatttag
 || ||||| || ||||||||| |||| |||||||| ||||||||||| ||||| ||  |||| |||||||| || || || || ||  | ||  | |||||  || |||   |   |||  || |||    ||  |||  |||  |      |                                                   
CTGCTCGGCACATATGTTGTGGATTGGAGAGCGCACGCGACAACTCGACGGAGCACACATTGAGTTCCTCCGAGGAGTAGCAAATCCCATTGGTGTTAAGgtacgcgttatctatctcttccttgtatccaatacctgacttctttgactcgcag--------------------------------------------------

upper sequence: GRMZM2G365160_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ24698 (Selaginella moellendorffii), 5'ss of exon 3

TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGACAACTCGATGGAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta---aatccttttttctatttgttaagtgaaatctaggcactatacttgtcctgtgatcctgactgtcaaatctacatgcaatttgtggaatttag
 || ||||| || ||||||||| |||| |||||||| ||||||||||| ||||| ||  |||| |||||||| || || || || ||  | ||  | |||||  || |||   |   |||  || |||    ||  |||  |||  |      |                                                   
CTGCTCGGCGCATATGTTGTGGATTGGAGAGCGCACGCGACAACTCGACGGAGCACACATTGAGTTCCTCCGAGGAGTAGCAAATCCCATTGGTGTCAAGgtacgcgttatctatctcttccttatatccaatacctgacttctttgactcgcag--------------------------------------------------

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|32839786|gb|CD979467.1|CD979467

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32840706|gb|CD980387.1|CD980387

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|38568918|gb|CF974803.1|CF974803

EST:     GAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG
genomic: GAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32841568|gb|CD981249.1|CD981249

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32840369|gb|CD980050.1|CD980050

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|38568956|gb|CF974841.1|CF974841

EST:     GAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG
genomic: GAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|71449372|gb|DR830422.1|DR830422

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|23357722|gb|BU645371.1|BU645371

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32841201|gb|CD980882.1|CD980882

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|149084700|gb|EE174190.2|EE174190

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32841042|gb|CD980723.1|CD980723

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32863018|gb|CF002700.1|CF002700

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|71533894|gb|DR784653.1|DR784653

EST:     ATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG
genomic: ATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32866393|gb|CF006075.1|CF006075

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32840781|gb|CD980462.1|CD980462

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|166636374|gb|EG280593.1|EG280593

EST:     CTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG
genomic: CTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32840997|gb|CD980678.1|CD980678

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

EST: gi|32840917|gb|CD980598.1|CD980598

EST:     GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTG

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: 250

TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGACAACTCGATGGAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagcttta ... tggaatttagGTGAGCGACAAAATGAACCCCAGTGAGTTGGTGAAGCTGATTGATATTCTGAACCCTTCAAACAAACCTGGAAGGATCACCATAATTACAAGGATGGGGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 285

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 666

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGACAACTCGATGGAGCTCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTGGGCATAAAGgtcagctttaaatccttttttctatttgttaagtgaaatctaggcactatacttgtcctgtgatcctgactgtcaaatctacatgcaatttgtggaatttag

- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA