ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttccatgttcagttttgaaagatgtacatgctgtacctgtctacctggttgtgtgggccgtgttgtgcagtaacatctctaggctattatgttga...

Basic information

species	Zea mays
transcript	GRMZM2G042623_T02
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G042623_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g01910.1 (Oryza sativa), 5'ss of exon 6

GCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttccatgttcagttttgaaagatgtacatgctgtacctgtctacctggttgtgtgggccg---tgttgtgcagtaacatctctaggctattatgttga
||||||||||||||||| |||||||||||||||||||||||||||||||||||| ||||||||||||||||| || || || |||||||| |||||||||||| |  |||||  || | ||| ||  ||||     |||| |  | |||||  |        ||    |  |     ||   | |  |    || | |   | 
GCATTGTGATGATCCTACAACACAGCAAATAATGATGGATGAGATTCTCCAGTCCGTTTGCTTGCTGGCTCAAGATCAATACGGCAACTACGTTGTTCAGgtctgccccatga-cattgttgcaaattgtatgatttgtatc-atataccttttgaacctaaccaaacttctagattgttttaccatttacatagtgtaacg-

upper sequence: GRMZM2G042623_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g74030.1 (Oryza sativa), 5'ss of exon 6

GCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttcca----tgttcagttttga----aagatgtacatgctgtacctgtctacctggttgtgtgggccg--tgttgtgcagtaacatctctaggctattatgttga
||||||||||||||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||   ||||||||||| ||||||||||| |||||||||  ||    | | |  |||||     | | || |  ||||     |    |||||         ||||  || |    | ||   | |||  ||||         
GCATTGTGATGATCCTAAAACCCAGCAAATCATGATGGATGAGATCCTACAATCTGTTTGCTTGCTGGCTACAGACCAGTATGGTAACTATGTTGTCCAGgtcagtgacaaaattttccctttttgtttttatggtggatttgctcctgttcagcacctgtcaactgtagccgcttgctaaaaaatagggtttct--gctac--------

upper sequence: GRMZM2G042623_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv13s0019g02000.t01 (Vitis vinifera), 5'ss of exon 6

GCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttccatgttcagttttgaaagatgtacatgctgtacct---gtctacctggttgtgtgggccg--tgttgtgcagtaacatctctaggctattatgttga
||| ||| ||||||| ||||| || |  |||||||||||||||||| | ||||||||  || || | |||||||| || ||||| || |||||||| |||||  |||  || |      ||| ||| | |   | |  | |||   || |   |   | || ||  |   |||||    |  | ||  || || |    ||    
GCACTGTCATGATCCAAAAACCCAACGTATAATGATGGATGAGATTTTGCAGTCTGTCCGCATGTTAGCTCAGGATCAATATGGGAATTATGTTGTACAGgtttgttgtattt-----cttgcaagctttttcttcaattcctcatgtttctttacatatggggttctgctgttggttggagaaatgacttggtttcattggcat

upper sequence: GRMZM2G042623_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S96_110V6.1 (Physcomitrella patens), 5'ss of exon 8

GCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttccatgttcagttttgaaagatgtacatgctgtacctgtctacctggt-tgtg-tgggccgtgttgtgcagtaacatctctaggctattatgt-tga
||||||    ||     | |  ||| |    || ||||| |||||  | |  ||   |||    |||||||||||||| || |||||||||||||| |||||  |     |||     |  |     |   ||  | ||   |||    | ||  | || |  | ||   | || |||    | ||| ||     | || || 
GCATTGCACGGACGAGCAGAAGCAGAAGGGTATCATGGAGGAGATATTGCGTTCCACTTGTACTCTGGCTCAGGACCAATACGGCAACTATGTTGTGCAGgtgggg---gtgtgtgtgtcgggcgtgttggcagtcggtgattgtggggcaggcgtatggttagacgaagtttgtagttgggtttctgggagtgcaggtatgg

upper sequence: GRMZM2G042623_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S35_216V6.1 (Physcomitrella patens), 5'ss of exon 8

GCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttccatgttcagttttgaaagatgtacatgctgtacctgtctacctggttgtgtgggccgtgttgtgcagtaacatctctaggctat---tatgttga--
||| ||    ||     | |  ||| |    || ||||| |||||| | |  ||    ||   ||||||||||||||||||||||||||||||||| ||||| ||     ||  | | | ||   |  ||| ||| | |    | | |  ||         |  |||    |   |    | |||| |   |   | | | ||  
GCACTGCACGGACGAGCAGAAGCAGAAGGGGATCATGGAAGAGATTTTACGTTCCACATGTACGCTGGCTCAGGACCAGTATGGCAACTATGTTGTACAGgtgaggggtgtga-cggctgtgtcggcagtatatggt-tgttggccga--tgaagagacaagttgtggaaggtt-tgttttttctaaggagtgcatgtatggaga

upper sequence: GRMZM2G042623_T02 (Zea mays), 5'ss of exon 7
lower sequence: EFJ20967 (Selaginella moellendorffii), 5'ss of exon 4

GCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttccatgttcagttttgaaagatgtacatgctgtacctgtctacctggttgtgtgggccgtgttgtgcagtaacatctctaggctattatgttga
|||||||   ||     | |  ||||||  ||| ||| | ||||| || | |||   ||||   || ||||||||||||||||| ||||||||||| |||||  |||   ||||   ||||      | | | | || |   |   | |||   | | |  |  ||| |||    |||    |      | |    ||  
GCATTGTACAGACGAACAGAAGCAGCAAGGAATAATGCAAGAGATACTGCGGTCAACTTGCAGTCTTGCTCAGGACCAGTATGGGAACTATGTTGTGCAGgttggtt--gtgtttctttttc-----ttttcttccttt--ttaatttcctttctttctctggtgtgctgtaagctaagtctttctttgtgtctctttag

upper sequence: GRMZM2G042623_T02 (Zea mays), 5'ss of exon 7
lower sequence: EFJ32290 (Selaginella moellendorffii), 5'ss of exon 4

GCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttccatgt--tcagttttgaaagatgtacatgctgtacctgtctacctggttgtgtgggccgtgttgtgcagta-acatctctaggctattatgttga
|||||||   ||     | | |||||||  ||| ||| | ||||| || |  ||   ||||   || ||||||||||||||||| ||||||||||| |||||  ||||  | |  |   ||||      | |  ||    |  || |||    |||  |||  ||   ||  | |  |     ||| |||             
GCATTGTACAGACGAACAGAAACAGCAAGGAATAATGCAAGAGATACTGCGATCAACTTGCAGTCTTGCTCAGGACCAGTATGGGAACTATGTTGTGCAGgttggttctgtttcttttcttttcttcctttttaatttcctttctttctctggggtgctgtaagctaagtctttctttgtgtctctttag-------------

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|78107326|gb|DV525744.1|DV525744

EST:     CCAGTATGGCAACTATGTTGTTCAG                         CATGTTCTGGAACATGGCAAACCCCATGAGAGATCAGCTATTATTGAGAAG
genomic: CCAGTATGGCAACTATGTTGTTCAGgtcagttcca ... aactccacagCATGTTCTGGAACATGGCAAACCCCATGAGAGATCAGCTATTATTGAGAAG

EST: gi|32935053|gb|CF039865.1|CF039865

EST:     AGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAG                         CATGTTCTGGAACATGGCAAACCCCATGAGAGATCAGCTATTATTGAGAAG
genomic: AGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttcca ... aactccacagCATGTTCTGGAACATGGCAAACCCCATGAGAGATCAGCTATTATTGAGAAG

EST: gi|5296192|gb|AI782872.1|AI782872

EST:     AGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAG                         CATGTTCTGGAACATGGCAAACCCCATGAGAGATCAGCTATTATTGAGAAG
genomic: AGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttcca ... aactccacagCATGTTCTGGAACATGGCAAACCCCATGAGAGATCAGCTATTATTGAGAAG

EST: gi|32935072|gb|CF039884.1|CF039884

EST:     AGTCTGTTCGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAG                         CATGTTCTGGAACATGGCAAACCCCATGAGAGATCAGCTATTATTGAGAAG
genomic: AGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttcca ... aactccacagCATGTTCTGGAACATGGCAAACCCCATGAGAGATCAGCTATTATTGAGAAG

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: 336

GCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACTATGTTGTTCAGgtcagttcca ... aactccacagCATGTTCTGGAACATGGCAAACCCCATGAGAGATCAGCTATTATTGAGAAGCTAATTGGCCAAATTGTGCAAATGAGCCAGCAAAAATTTGCCTCAAATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187