ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGAGAGTCGCAGGCGACAACTCCAGGATATGATTGAAGAGGCCATCAGTAACAATGGCAATAAAACCTACCTGCACATTCTCAGCCAGTACAGACTACTTgtaagtaacccacaactttgtagtctatcccgatttaagcaataagaatgtgacatctcacatgctatctatgtgtaataaactatttag

Basic information

species	Zea mays
transcript	GRMZM5G837018_T01
intron #	14
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G837018_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os03g56260.1 (Oryza sativa), 5'ss of exon 14

TGAGAGTCGCAGGCGACAACTCCAGGATATGATTGAAGAGGCCATCAGTAACAATGGCAATAAAACCTACCTGCACATTCTCAGCCAGTACAGACTACTTgtaagtaacccacaactttgtagtctatcccgatttaagcaataagaatgtgacatctcacatgctatctatgtgtaataaactatttag
|||||||||||  || |||||||| |||||||| || || |||| ||||||||||||||| | ||||||||| ||||||||||| ||||||||||| ||||| ||||||| || || || |||| | |     |       |||| | | ||| |   ||||  ||   ||||  ||||      |||||
TGAGAGTCGCAAACGTCAACTCCAAGATATGATCGAGGAAGCCACCAGTAACAATGGCAACAGAACCTACCTCCACATTCTCAGTCAGTACAGACTTCTTgtgagtaacc-accacattttagtatgttttcctc------ataatagt-tgatactccacaatctgcttatggataatgtgtgttttag

upper sequence: GRMZM5G837018_T02 (Zea mays), 5'ss of exon 14
lower sequence: Vv07s0205g00140.t01 (Vitis vinifera), 5'ss of exon 14

TGAGAGTCGCAGGCGACAACTCCAGGATATGATTGAAGAGGCCATCAGTAACAATGGCAATAAAACCTACCTGCACATTCTCAGCCAGTACAGACTACTTgtaagta-acccacaactttgtagtctatcccgatttaagca-ataagaatgtgacatctcacatgctatctatgtgtaataaactatttag---------
|||||  |  ||  | || || ||  | |||||||| || ||||| ||||| |||||||| ||||||||| ||||||||||||| || ||||| || || ||||||| |   |   || | |  | | |    |   ||  |  ||| | |     |  | | ||||| |  || |   | |     |||           
TGAGAAGCAAAGATGCCAGCTTCAAAACATGATTGATGAAGCCATTAGTAATAATGGCAACAAAACCTACTTGCACATTCTCAGTCAATACAGGCTCCTGgtaagtagatataaggctgttttctttctatataccaaaatatgtaatagtcctgaaattta-atgctgtgaatttagcaaatttggtttcagtatgaaaa

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|32928858|gb|CF033670.1|CF033670

EST:     ACAGACTACTT                         GGAATGACTAACGCTGAACTTCAAATTGAGATGGCTATGCGGGATCAAGTT
genomic: ACAGACTACTTgtaagtaacc ... aactatttagGGAATGACTAACGCTGAGCTTCAAATTGAGATGGCTATGCGGGATCAAGTT

EST: gi|32929234|gb|CF034046.1|CF034046

EST:     ACAGACTACTT                         GGAATGACTAACGCTGAACTTCAAATTGAGATGGCTATGCGGGATCAAGTT
genomic: ACAGACTACTTgtaagtaacc ... aactatttagGGAATGACTAACGCTGAGCTTCAAATTGAGATGGCTATGCGGGATCAAGTT

EST: gi|32929010|gb|CF033822.1|CF033822

EST:     GTACAGACTACTT                         GGAATGACTAACGCTGAACTTCAAATTGAGATGGCTATGCGGGATCAAGTT
genomic: GTACAGACTACTTgtaagtaacc ... aactatttagGGAATGACTAACGCTGAGCTTCAAATTGAGATGGCTATGCGGGATCAAGTT

EST: gi|32929217|gb|CF034029.1|CF034029

EST:     ACAGACTACTT                         GGAATGACTAACGCTGAACTTCAAATTGAGATGGCTATGCGGGATCAAGTT
genomic: ACAGACTACTTgtaagtaacc ... aactatttagGGAATGACTAACGCTGAGCTTCAAATTGAGATGGCTATGCGGGATCAAGTT

EST: gi|32928591|gb|CF033403.1|CF033403

EST:     ACAGACTACTT                         GAAATGACTAACGCTGAACTTCAAATTGAGATGGCTATGCGGGATCAAGTT
genomic: ACAGACTACTTgtaagtaacc ... aactatttagGGAATGACTAACGCTGAGCTTCAAATTGAGATGGCTATGCGGGATCAAGTT

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: 128

TGAGAGTCGCAGGCGACAACTCCAGGATATGATTGAAGAGGCCATCAGTAACAATGGCAATAAAACCTACCTGCACATTCTCAGCCAGTACAGACTACTTgtaagtaacc ... aactatttagGGAATGACTAACGCTGAGCTTCAAATTGAGATGGCTATGCGGGATCAAGTTATACATAATCAGAGGGAAGCTCTAAGGAGCCTGTGGAACATTCTCTATG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 17

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 19