ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgtatttctgctctccagagacatattagttgcagatttttctctaatgatgctcattatagcttattgcactgttctatactctattattacag

Basic information

species	Zea mays
transcript	GRMZM2G000177_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G000177_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g46510.2 (Oryza sativa), 5'ss of exon 9

AGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgtatttctgctctccagagacatatta-gttgcagatttttctctaatg-------atgctcattatagcttattgcactgttctatactctatt----attacag
| ||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||| |||||||| |     || |  |  || |||| | | |  |||| ||| | || ||        |    || ||  ||||   | ||| ||  |  | | ||     ||||||
AACCAGTACCTAAACTTGCTTGCCATAGTGTTGCATCGTGGTGTCATCCTCGTGCACCAAACCTTGATATTCTGACTTGTGTCAAGGACTCCCATATATGgtatgt-tcctgactttggaaggaaatatcaagctatagatattt-tatagtgctttcaagtttcaataatgacttacctctctgatccctcttttgttttgtgttacag

upper sequence: GRMZM2G000177_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA19G41130.1 (Glycine max), 5'ss of exon 9

AGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgtatttctgctctcca---gagacatattagttgcagat---ttttctctaatgatgctcattatagcttat-tgcactgt-tctatactctattattacag-------------
||||||| || ||| | ||||| || ||||| || || ||||| ||||| || || ||||||||||||||||||||||| ||||| || || || || ||||||||| |  |  |   ||   |     | | ||||    ||   |||| | | || ||| |    ||    ||| | || | | |  |||    ||| | |  |             
AGCCAGTTCCCAAATTGGCTTGCCACAGTGTGGCTTCTTGGTGCCATCCTCGAGCTCCAAACCTTGATATTCTAACTTGCGTCAAAGATTCTCACATATGgtatgtagtcttctttctcatttggtggctttaagttttttatattttttatttgataatg-tggccatgcactatattcattatatacataaagaattttaattgaaatttttgttag

upper sequence: GRMZM2G000177_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G38530.1 (Glycine max), 5'ss of exon 9

AGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgta-tttctgctctccagagacatattag----ttgcagatttttc-tctaatgatgctcattatagcttat-tgcactgt-tctatactctattattacag-------------
||||||| || ||| | ||||| || ||||| || || ||||||||||| || || ||||||||||||||||||||||| ||||| || || || || ||||||||| |||    |||||   |     |||     | | | ||||||  | | ||  || | |  ||    ||| | || | | | ||||    ||| | |                
AGCCAGTTCCCAAATTGGCTTGCCACAGTGTGGCTTCTTGGTGTCATCCTCGAGCTCCAAACCTTGATATTCTAACTTGCGTCAAAGATTCTCACATATGgtatgtagttttctttctcctttggtggcttaaagtttcgtatattttttatttgatagtg-tgaccatgcactatattcattatatatataaagaattttaattttaatttttgttag

upper sequence: GRMZM2G000177_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT5G24710.1 (Arabidopsis thaliana), 5'ss of exon 9

AGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgtatttctgctctccagagacatat-tagttgcagatttttctcta-at--gatgctcattatagcttattgcactgttctatactctattattacag
| || || || ||||| ||||| || ||||||||||| |||||||| || || || ||||||||||||||| | ||||| || || || || || || |||||| | | | |    |   |     ||| | || | | || ||| | || ||  ||||     | ||  |  ||| | | ||  |                
AACCTGTCCCGAAACTAGCTTGCCACAGTGTTGCATCTTGGTGTCACCCTCGAGCGCCAAACCTTGATATTTTGACTTGCGTTAAAGATTCACACATATGgtatctttgtttaagatttggtattgtatatggtagaatatatttatgtatattagatgagtggtctaattgtttgaatttttgcag---------------

upper sequence: GRMZM2G000177_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv08s0056g00040.t01 (Vitis vinifera), 5'ss of exon 10

AGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgtatttctgctctccagagacatattagttgcagatttttctctaatgatgctcattatagct-----tattgca-ctgttctatactcta-ttattacag
| || || || || || ||||| |||||||| || || ||||| || || || || ||||||||||||||  ||||||||||||| || ||||| |||||||||| ||||   ||  |  |  |     | |||  | ||||   |       |  || |||| |||     ||  ||| ||  | || ||   | || | |   
AACCTGTTCCAAAGCTGGCTTGCCATAGTGTGGCGTCTTGGTGCCACCCTCGAGCTCCAAACCTTGATATCTTAACTTGTGTCAAAGATTCCCACATTTGgtatgcattttctcttcctggcaatg---ttgttaaaaatttccattagtgtgtattctttattgctgtgattagggcaactcgtttaaacaggaattctcat--

upper sequence: GRMZM2G000177_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ13686 (Selaginella moellendorffii), 5'ss of exon 9

AGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgtatttctgctctccagagacatattagt-tgcagatttttctctaatgatgctcattatagcttattgcactgttctatactctattattacag
||||  | || ||| |||| ||||| |||||||| || ||||| ||||| ||||| || ||| | || || || |||||||| |||||||| ||||||||||| ||  || || | |         |||| || | || | ||||  ||  ||  |                                           
AGCCCATTCCAAAAGTTGCGTGTCAAAGTGTTGCCTCCTGGTGCCATCCTCGTGCCCCCAACGTGGACATCCTGACTTGTGTGAAGGACTCACATATTTGgtacgtgcttttggtat------gtctattggtctacaaagtttttgcttctgcag-------------------------------------------

upper sequence: GRMZM2G000177_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ28983 (Selaginella moellendorffii), 5'ss of exon 9

AGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgtatttctgctctccagagacatattagt-tgcagatttttctctaatgatgctcattatagcttattgcactgttctatactctattattacag
||||  | || ||| |||| ||||| |||||||| || ||||| ||||| ||||| || ||| | || || || |||||||| |||||||| ||||||||||| ||  || || | |         |||| || | || | ||||   |  ||  |                                           
AGCCCATTCCAAAAGTTGCGTGTCAAAGTGTTGCCTCCTGGTGCCATCCTCGTGCCCCCAACGTGGACATCCTGACTTGTGTGAAGGACTCACATATTTGgtacgtgcttttggtat------gtctattggtctacaaagtttttgtttctgcag-------------------------------------------

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|60346425|gb|DN213398.1|DN213398

EST:     CGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTG                         GGCCATAGAACACCCAACTTATTCTGCTTTAACAAGACCGCTCTGCGAACT
genomic: CGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgtattt ... attattacagGGCCATAGAACACCCAACTTATTCTGCTTTAACAAGACCGCTCTGCGAACT

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: 339

AGCCAGTGCCTAAACTTGCTTGTCATAGTGTTGCATCGTGGTGTCATCCCCGTGCACCAAACCTTGATATTCTAACTTGTGTCAAGGACTCCCATATTTGgtatgtattt ... attattacagGGCCATAGAACACCCAACTTATTCTGCTTTAACAAGACCGCTCTGCGAACTGTCATCACTTGTTCCTCCACAGGTTCTTGCACAGCATAAGAAACTGAGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112