ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtgtgcatcacgttttgttgtatttgcatattggttgcaacgtgtatggtcgaaataattatcacatactaaatcatacgttttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGCCG

Basic information

species	Zea mays
transcript	GRMZM2G113137_T01
intron #	12
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g62090.1 (Oryza sativa), 3'ss of exon 12

gtaag-tgtgcatcacgttttgttgtatttgcatattggttgcaacgtgtatggtcgaaataattatcacatactaaatcatacgttttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGCCG
||||  | || | || | ||   ||| || |      ||| | ||  | |   ||     ||  |   | |   ||| |  |  || || ||  ||||||| ||||| || ||||| || ||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| |
gtaaaatttggagcatggttg--tgtgttagttggcaggtcg-aatatcttccgt-----taccttgtaaaccataacttctttgtctttttgtagATTGGCTGGATCTACGGATCCGTTACAGAGGATATTCTTACTGGGTTTAAGATGCACTGCCATGGTTGGCGGTCGATTTACTGCATACCTAAGCGGGCTG

upper sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12

-----gtaagtgt-gcatcacgttttgttgtatt--tgcatattggttgcaacgtgtatggtcgaaataattatcacatactaaatcatacgttttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGCCG-
      || || | ||||  |    |||    ||  ||  |||   ||  | | ||| |      ||   | |  ||  |||  ||  | | |||| || ||| | |||||||| |||||||| || |||||||||||  | || || ||||| ||||| |||||||| ||||| || || |||||||| ||| | | ||||  
tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcat--tgccttttatt-cagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGA-CAGGCCAG

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|32831131|gb|CD970809.1|CD970809

EST:     TACATGTCATCAGTTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGAT                         ATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG
genomic: TACATGTCATCAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGATgtaagtgtgc ... tttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG

EST: gi|78180701|gb|DV551074.1|DV551074

EST:     TACATGTCATCAGTTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGAT                         ATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG
genomic: TACATGTCATCAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGATgtaagtgtgc ... tttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG

EST: gi|6859987|gb|AW355981.1|AW355981

EST:     TACATGTCATCAGTTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGAT                         ATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG
genomic: TACATGTCATCAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGATgtaagtgtgc ... tttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG

EST: gi|101387279|gb|EB815656.1|EB815656

EST:     CAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGAT                         ATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG
genomic: CAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGATgtaagtgtgc ... tttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG

EST: gi|32868679|gb|CF008361.1|CF008361

EST:     TACATGTCATCAGTTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGAT                         ATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG
genomic: TACATGTCATCAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGATgtaagtgtgc ... tttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG

EST: gi|32830704|gb|CD970382.1|CD970382

EST:     TACATGTCATCAGTTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGAT                         ATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG
genomic: TACATGTCATCAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGATgtaagtgtgc ... tttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG

EST: gi|32941340|gb|CF046159.1|CF046159

EST:     TACATGTCATCAGTTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGAT                         ATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG
genomic: TACATGTCATCAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGATgtaagtgtgc ... tttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG

EST: gi|12045848|gb|BF728091.1|BF728091

EST:     TACATGTCATCAGTTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGAT                         ATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG
genomic: TACATGTCATCAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGATgtaagtgtgc ... tttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAG

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: 45 (upstream exon), 48 (downstream exon)
Score: 223

TGGTGGAACCCTGAAGAGTGCCAGTCCAGCTTCTCTTCTGAAGGAAGCTATACATGTCATCAGCTGTGGATATGAAGACAAAACAGGCTGGGGAAAAGATgtaagtgtgc ... tttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGCCG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 424

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 378

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 365

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcaacgtgtatggtcgaaataattatcacatactaaatcatacgttttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGCCG