ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagcattacatgatggccatttacagattcactgataattattttgcccccccccccccccccccccccccccccgagtttctacttatgcatttcccaactcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGCTCAGCACCATTCATGTCATGTATGGTTTGTTGCACATCCTAGACAG

Basic information

species	Zea mays
transcript	GRMZM2G164835_T01
intron #	17
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G164835_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os06g45980.1 (Oryza sativa), 3'ss of exon 17

gtaagcattacatgatggccatttacagattcactgataattattttgcccccccccccccccccccccccccccccgagtttctacttatgcatttcccaactcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGCTCAGCACCATTCATGTCATGTATGGTTTGTTGCACATCCTAGACAG
     ||   | | |   ||    ||||  |       ||  ||    | |  | | |   | |    |  |        |||    |  || |||   | | |    |||| || ||||||||||||||||| ||||| || |||||||||||||| ||||||||||||||||| |||||||| ||||||||||| || |||||||||
-----caaccc-tcaccaccgaacacagccttggcctcaaccat---actcggctctcaagcacttaacttcatgtttgcttttccttactgtattgtgccatt---gacagAACCGAAACAGAATATGTCAGTCAGATGCTTACCAAGATTAAGCGGTTTGCTCAGCACCATTCTTGTCATGTTTGGTTTGTTGCCCACCCTAGACAG

upper sequence: GRMZM2G164835_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA09G03310.1 (Glycine max), 3'ss of exon 11

gtaagcattacatgatggccatttacagattcactgataattattttgcccccccccccccccccccccccccccccgagtttctacttatgcatttcccaactcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGCTCAGCACCATTCATGTCATGTATGGTTTGTTGCACATCCTAGACAG
          | ||||     |||       ||   |   ||||| |   |                             | |  | ||||   || |  |  |     |||||| |||||||||||||| |||||||| || |||   || ||||| ||||| || || |||  ||| ||||| |||||||| ||||||||||| |||
--------accctgattattctttctgttgccagctacctttattgttgtctagataatggatggataattgattattgatgttaatttatttgttgcaaacat----gcagGACTGAAACAGAATATGTGAGCCAGATGCTTACCTTAATCAAGCGTTTTGCCCAACATCATGGATGCCATGTTTGGTTTGTGGCACATCCTAGGCAG

upper sequence: GRMZM2G164835_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv10s0003g05490.t01 (Vitis vinifera), 3'ss of exon 17

gtaagcattacatgatggccatttacagattcactgataattattttgcccccccccccccccccccccccccccccgagtttctacttatgcatttcccaactcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGCTCAGCACCATTCATGTCATGTATGGTTTGTTGCACATCCTAGACAG
              ||  |   | | |    |  || || ||     || || |        |   |          |||    | |  |  | |  || ||      |||||||||||||||| ||||| || ||||| ||||| | ||| ||||| ||||||||||| || || ||||| || |||||||| |||||||||||||||
-----------tccatttcttctcatactccctttgttactttgagggctcctcttatggtgcattctataaatttagagagcatcccaacac-taacctaatgtgttacagGACGGAAACAGAGTATGTGAGTCAGATGCTGACAATGATCAAGCGATTTGCTCAGCATCACTCTTGTCACGTTTGGTTTGTAGCACATCCTAGACAG

upper sequence: GRMZM2G164835_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv18s0001g01350.t01 (Vitis vinifera), 3'ss of exon 4

gtaagcattacatgatggccatttacagattcactgataattattttgcccccccccccccccccccccccccccccgagtttctacttatgcatttcccaactcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGCTCAGCACCATTCATGTCATGTATGGTTTGTTGCACATCCTAGACAG
         |  | |   ||||||    || | |   || ||     || || |        |   |          |||    | |  |    |  || ||      ||||||| |||||||| ||||| || ||||| || || |  || || || ||||||||||| || || |||||||| |||||||| || ||||||||||||
---------atttaa-atccatttcttcatactccc-tactttgagagctcctcttatggtgcattctataaatttagagagcatcccaacat-taacctaatgtgttacagGACAGAAACAGAGTATGTGAGTCAGATGCTAACAATAATCAAACGATTTGCTCAGCATCACTCTTGTCATGTTTGGTTTGTAGCGCATCCTAGACAG

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|32803200|gb|CD955436.1|CD955436

EST:     GATCCTTATAATGAACTTGACCATCAGCGCCCCTCAAACCA                         GACGGAAACAGAATATGTCAGCCAGATTCTTACCAAGATTA
genomic: GATCCTTATAATGAACTTGACCATCAGCGCCCCTCAAACCAgtaagcatta ... ctcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTA

EST: gi|76917406|gb|DV166826.1|DV166826

EST:     CTGGTGATAGATCCTTATAATGAACTTGACCATCAGCGCCCCTCAAACCA                         GACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGC
genomic: CTGGTGATAGATCCTTATAATGAACTTGACCATCAGCGCCCCTCAAACCAgtaagcatta ... ctcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGC

EST: gi|31350470|gb|CD434827.1|CD434827

EST:     CTGGTGATAGATCCTTATAATGAACTTGACCATCAGCGCCCCTCAAACCA                         GACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGC
genomic: CTGGTGATAGATCCTTATAATGAACTTGACCATCAGCGCCCCTCAAACCAgtaagcatta ... ctcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGC

EST: gi|89760436|gb|DY688849.1|DY688849

EST:     CTGGTGATAGATCCTTATAATGAACTTGACCATCAGCGCCCCTCAAACCA                         GACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGC
genomic: CTGGTGATAGATCCTTATAATGAACTTGACCATCAGCGCCCCTCAAACCAgtaagcatta ... ctcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGC

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: 344

GGGTTCTTGACCTTGCGAAAGCTGCAGTTCTAAGACATGGAGTGCGTGGTCTGGTGATAGATCCTTATAATGAACTTGACCATCAGCGCCCCTCAAACCAgtaagcatta ... ctcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGCTCAGCACCATTCATGTCATGTATGGTTTGTTGCACATCCTAGACAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 77

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 60

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ccccccccccccccccccccgagtttctacttatgcatttcccaactcacaacagGACGGAAACAGAATATGTCAGCCAGATTCTGACCAAGATTAAGCGCTTTGCTCAGCACCATTCATGTCATGTATGGTTTGTTGCACATCCTAGACAG