ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AACAGCCAGTACTGAAGAAAAGGACATGGTTTTTTCAGAAATTATGCCTCAAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgtatggaagtgctgcctggatatctgtctgaggttgtcttgtatcttttgttaactcggtgctcctttttctcag

Basic information

species	Zea mays
transcript	GRMZM2G012964_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G012964_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g01910.1 (Oryza sativa), 5'ss of exon 3

AACAGCCAGTACTGAAGAAAAGGACATGGTTTTTTCAGAAATTATGCCTCAAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgtatggaagtgctgcctggatatctgtctgaggttgtcttgtatcttttgttaactcggtgctcctttttctcag
||| |||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||| || ||||| ||||||||||||||||||||||| || ||||||   | ||   |  |     | |  || ||| ||    |||   ||||      | ||      ||    | |||    ||
AACGGCCAGTACTGAAGAGAAGGACATGGTCTTTTCAGAAATCATGCCTCAAGCTCTCACGTTGATGACCGATGTATTTGGAAATTATGTTGTTCAGAAGgtaaaggggttaaggggaaaaacata-atctct-tcaagtgttactttgtgataaatattcttatagtttgtcatttgactag

upper sequence: GRMZM2G012964_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g74030.1 (Oryza sativa), 5'ss of exon 3

AACAGCCAGTACTGAAGAAAAGGACATGGTTTTTTCAGAAATTATGCCTCAAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgtatggaagtgctgcctggatatctgtctga-ggttgtcttgtatct-tttgttaactcggtgctcctttttctcag
||||||||| ||||||||||| |||||||||||| | ||||| |||||||| ||||||||||| ||||||||||| |||||||| |||||||| || ||||||        ||  |    |   |   | || || | |  |   || ||  | |    | | ||   ||  ||||||    |||
AACAGCCAGCACTGAAGAAAAAGACATGGTTTTTGCTGAAATCATGCCTCAGGCTCTCACATTGATGACTGATGTCTTTGGAAACTATGTTGTTCAGAAGgtac-------tgataacatttttt---tgtcagtataatagccatcatgattttacccgctgac--agtaatcctttgaaccag

upper sequence: GRMZM2G012964_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0019g02000.t01 (Vitis vinifera), 5'ss of exon 3

AACAGCCAGTACTGAAGAAAAGGACATGGTTTTTTCAGAAATTATGCCTCAAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgtatgg------aagtgct-gcctggatatctgtctgaggttgtcttgtatcttttgttaact-cggtgctcctttttctcag----------------------------
 || || |  || ||||||||||||||||||||    ||||||||||| ||||| ||  |  ||||||||||||| ||||| || |||||  |||| |||||||    || | |      | | ||| |  |    || | | || | ||||  |  | ||   || || | | |     |||||    |                             
GACTGCAACAACAGAAGAAAAGGACATGGTTTTCCATGAAATTATGCCCCAAGCCCTTTCTCTAATGACTGATGTCTTTGGTAACTATGTGATCCAGAAGgtagcttggttttgccttccatgagcttgttttagcatgt-tatgtgattgtgctaaagctaaagtaaattgcagaataacttttatgtatggctaacatttgatgtttgtcttttcag

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|87153253|gb|DY398042.1|DY398042

EST:     AAGCTCTCACATTGATGACTGATGTATTTGGAAATTATGTTGTCCAAAAG                         TTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAAT-GGCTGGTCAGCTT
genomic: AAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgt ... tttttctcagTTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAATTGGCTGGTCAGCTT

EST: gi|17921887|gb|BM259538.1|BM259538

EST:     AAGCTCTCACATTGATGACTGATGTATTTGGAAATTATGTTGTCCAAAAG                         TTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAATTGGCTGGTCAGCTT
genomic: AAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgt ... tttttctcagTTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAATTGGCTGGTCAGCTT

EST: gi|17921559|gb|BM259210.1|BM259210

EST:     AAGCTCTCACATTGATGACTGATGTATTTGGAAATTATGTTGTCCAAAAG                         TTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAATTGGCTGGTCAGCTT
genomic: AAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgt ... tttttctcagTTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAATTGGCTGGTCAGCTT

EST: gi|211406262|gb|FL311355.1|FL311355

EST:     AAGCTCTCACATTGATGACTGATGTATTTGGAAATTATGTTGTCCAAAAG                         TTTTTTGAGCATGGAAGCACTACCCAGATAAAGGAATTGGCTGGTCAGCTT
genomic: AAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgt ... tttttctcagTTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAATTGGCTGGTCAGCTT

EST: gi|17970204|gb|BM276968.1|BM276968

EST:     AAGCTCTCACATTGATGACTGATGTATTTGGAAATTATGTTGTCCAAAAG                         TTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAATTGGCTGGTCAGCTT
genomic: AAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgt ... tttttctcagTTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAATTGGCTGGTCAGCTT

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), 49 (downstream exon)
Score: 279

AACAGCCAGTACTGAAGAAAAGGACATGGTTTTTTCAGAAATTATGCCTCAAGCTCTCACATTAATGACTGATGTATTTGGAAATTATGTTGTCCAAAAGgtaggagtgt ... tttttctcagTTTTTTGAGCATGGAAGCACTGCCCAGATAAAGGAATTGGCTGGTCAGCTTATTGGACGTGTCCTTGCTCTTAGTCTTCAGATGTATGGGTGCCGGGTTA

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 111

Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 117