ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagctgcaatattatgatatttttaatatattttatttatacaatgctatcgggagtgactcttgtttgttttatag

Basic information

species	Zea mays
transcript	GRMZM2G037200_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G037200_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g45480.4 (Oryza sativa), 5'ss of exon 6

GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagctgcaatattatgatatttttaatatattttatttatacaatgctatcgggagtgactcttgtttgttttatag
|| ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| |||||| |||||||||||||||||||  ||||||| ||||||||||||| ||| ||   |  || |||  ||||      ||||| || |    |  |||| | |||| ||| | || | ||| |||
GGAGCACTTGCCCTAAGTGGCATGCCTGATGCACAATCAAAACCTGTGCTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagttgtcttgctaagattattttg-----ttttacttctgatgt-ttatctgaagtggctccttttgggtttgtag

upper sequence: GRMZM2G037200_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g45480.3 (Oryza sativa), 5'ss of exon 4

--GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagctgcaatattatgatatttttaatatattttatttatacaatgctatcgggagtgactcttgtttgttttatag
  || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| |||||| |||||||||||||||||||  ||||||| ||||||||||||| ||| ||   |  || |||  ||||      ||||| || |    |  |||| | |||| ||| | || | ||| |||
AGGGAGCACTTGCCCTAAGTGGCATGCCTGATGCACAATCAAAACCTGTGCTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagttgtcttgctaagattattttg-----ttttacttctgatgt-ttatctgaagtggctccttttgggtttgtag

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|211273334|gb|FL390033.1|FL390033

EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|211495269|gb|FL457209.1|FL457209

EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|29576813|gb|CB616925.1|CB616925

EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|71429256|gb|DR810306.1|DR810306

EST:     CTTCTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|149095549|gb|EE181206.2|EE181206

EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|149086360|gb|EE175901.2|EE175901

EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|211403681|gb|FL424159.1|FL424159

EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|60347714|gb|DN214687.1|DN214687

EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|31997695|gb|CD661718.1|CD661718

EST:     CTACTGTGTTCATTAAATGACAACNCTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|5847063|gb|AW000142.1|AW000142

EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

EST: gi|211527293|gb|FL400210.1|FL400210

EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA

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: 103

GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACAGATGGGTCCTGGTGGTTTATTTTTTACCGGGGATGGAACTGGTGAGCTC

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 73

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66