ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgtattggcctgcaattcagtttacttgacaggactagcactgcttctaacatttttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT

Basic information

species	Zea mays
transcript	GRMZM2G078576_T04
intron #	13
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 13

gtatgtattggcctgcaattcagtttact----------tgacaggactagcactgcttctaacatttttgt--acagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT
||||||  || |  ||||||   ||||||          |     || ||  ||||||||||| || | | |  |||||| || |||||| | ||||||||||||||||| ||| ||||||| ||||| ||||| || || |||||| |||||||||| || ||||| 
gtatgtgctgactagcaattatatttactctgtacctcatagggagaatactactgcttctaatatgtgtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA

upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA20G28880.1 (Glycine max), 3'ss of exon 12

--------------------------------------------------gtatgtattggcctgcaattcagtttac-----ttgacaggactagcactg-cttctaacatttttgta-cagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT
                                                  || || | |     | |||| |  |||      ||  ||    |   ||||  ||||    |   ||   ||||| || |||||  || ||||  | || || || ||| ||||||| || |||||||||||||| ||||||||| |||| ||||| || |||
gtaaacgattttgattgattgagaagatttatcatgtctatttttatctagtttgcagtaata-gaaatttacattataaccttttgcatctatcttactgatttcttgtgtgactggggcagGTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGTTTCAATGAACTGATTGATAACATTTATACT

upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 13
lower sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 13

--------------------------------------------------gtatgtattg---gcctgcaattcagttta----cttgacaggactagcactgcttctaacatt--tttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT
                                                   ||||| |        | ||| ||   |||    |||  || |  |   |    | || ||  |  ||||  ||||||||||||||  || ||||  |||| ||||| ||| |||| || || ||||||||||| || ||||| |||||||| || || ||||||
gtatcatcatttgtttgtgtggcaactaatacattatagacttgtatctgttatgtctcacaaatatacaaatcttattagcaccttttcatgctttataaaattactcactgtattttgggcagGTTGTATATGCAATAATGCACAGACAGGAGGTCTTTCAGCCTTTCAAGAATCATCCACGATTCAATGAGCTGCTTGAAAATATCTACACT

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|26558732|gb|CA830967.1|CA830967

EST:     TCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAG                         GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT
genomic: TCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAGgtatgtattg ... ttttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT

EST: gi|87155515|gb|DY400304.1|DY400304

EST:     TGGAAATAATCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAG                         GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT
genomic: TGGAAATAATCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAGgtatgtattg ... ttttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT

EST: gi|78111274|gb|DV529671.1|DV529671

EST:     AATCCTTACATATGCATTGCCCAGAAATCCCGAG                         GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT
genomic: AATCCTTACATATGCATTGCCCAGAAATCCCGAGgtatgtattg ... ttttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT

EST: gi|32793737|gb|CD945973.1|CD945973

EST:     TGGAAATAATCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAG                         GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTA
genomic: TGGAAATAATCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAGgtatgtattg ... ttttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTA

EST: gi|22472877|gb|BU037357.1|BU037357

EST:     AGAAATCCCGAG                         GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT
genomic: AGAAATCCCGAGgtatgtattg ... ttttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT

EST: gi|93282383|gb|EB674647.1|EB674647

EST:     TGGAAATAATCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAG                         GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT
genomic: TGGAAATAATCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAGgtatgtattg ... ttttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAAT

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: 48 (upstream exon), 48 (downstream exon)
Score: 138

TCTACAGAGCTTCACATATATACAGATTTCTTGAGAATTGTTCTGGAAATAATCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAGgtatgtattg ... ttttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 84

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 140

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cctgcaattcagtttacttgacaggactagcactgcttctaacatttttgtacagGTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT