ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatcccccagagctttcttttcaccttttgtttcttactgtttgttttaatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG

Basic information

species	Selaginella moellendorffii
transcript	EFJ11904
intron #	16
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: EFJ11904 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: LOC_Os01g72340.2 (Oryza sativa), 3'ss of exon 17

-----------------------------------------------------------------------------gtatcccccagagctttc--ttttcaccttttgtttcttactgt------ttgttttaatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG
                                                                             ||| |    | | ||||   || | |  |   | |  || | |       |||  ||  |  ||||||||||| ||||||||||||||||||||  | || || || || || |||   || ||||| |||||  ||||| |  |    ||    |  ||||  ||  
gttcgcatttgcactgtgtttagataaacaaaagctttattgaactcaacgaattacattaagatgatgatagaattgtaccgataacaacttttgattgtgatttggcgatgatttcagagagaaattgggtttgtg-ttgcagGTGCATCTTGATCACAAGCACATGGGGCTGGGAGGGGACGACAGCTGGTCGCCGTGCGTGCACGAGCAGTACTTGCTGCCGCCGGCGAGATACGCCTTCT

upper sequence: EFJ11904 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 17

---------------------------------------------------------------------------------gtatcccccagagctttc--ttttcaccttttgtttcttactgt------ttgttttaatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG
                                                                                 ||| |    | | ||||   || | |  |   | |  || | |       |||  ||  |  ||||||||||| ||||||||||||||||||||  | || || || || || |||   || ||||| |||||  ||||| |  |    ||    |  ||||  ||  
gtgggttcgcatttgcactgtgtttagataaacaaaagctttattgaactcaacgaattacattaagatgatgatagaattgtaccgataacaacttttgattgtgatttggcgatgatttcagagagaaattgggtttgtg-ttgcagGTGCATCTTGATCACAAGCACATGGGGCTGGGAGGGGACGACAGCTGGTCGCCGTGCGTGCACGAGCAGTACTTGCTGCCGCCGGCGAGATACGCCTTCT

upper sequence: EFJ11904 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GLYMA15G37670.1 (Glycine max), 3'ss of exon 11

-----------------------gtatcccccagagc----tttcttttcaccttttgtttcttactgtttgtt----ttaatactt---------gcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGT-CTTACCACGAAATTACGAGTTTG
                        |||  |||| |      ||  |||| |   ||  | |  | | |||| ||    |||||   |          ||| | || || ||||||||||||||||| || ||||| ||||||||||||   || || |||||| |  ||||  |  | | | |   |  ||    | | | 
tcctatttacaggaactaaaaatatatttcccaaattattattattttttattattattattgtgcagtttattatgtttaatgtcttatgggatcacagATTCATCTGGATCACAAGCACATGGGATTGGGTGGAGATGATAGTTGGTCACCATGTGTCCACAAACAGTATTTGATTCCTCCTGTGCCATACTCATTCT-

upper sequence: EFJ11904 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GLYMA13G26700.1 (Glycine max), 3'ss of exon 17

------------------------------------gtatcccccagagctttcttttcaccttttgtttcttactgtttgttttaatac----ttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGT-CTTACCACGAAATTACGAGTTTG
                                     | |          |   | | ||  || |  |  ||| ||| |  | |  ||     |||||| | || || ||||||||||||||||| || ||||| ||||||||||||   || || ||||||||  ||||  |  | | | |   |  ||    | | | 
ttacaagaagtaaaaatatatttagcccaaattatttttttttttcatattaattatgcaatttatcatctttaatgtcttatctcttatggcattgcagATTCATCTAGATCACAAGCACATGGGATTGGGTGGAGATGATAGTTGGTCGCCATGTGTCCACGAACAGTATTTGATTCCTCCTGTGCCATACTCATTCT-

upper sequence: EFJ11904 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: Vv13s0067g03000.t01 (Vitis vinifera), 3'ss of exon 16

-----------------------------------gtatcccccagagctttcttttcaccttttgtt-tcttactgt-ttgtttta---atacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG
                                    | | ||   |    |  || | |  |   ||   |||  | | ||||| |     |  |  |||||||| || || ||||||||||||||||| ||||| |||||||| |||  |||||| ||||| ||  | |||||  |   | |       |||   ||  
catgctacctgcctgcagctttccctgttcttgatttgttccttggcatatcattgttatttccagtcaccttgttatattgttatggcggtgttcccagGTGCATCTGGACCACAAGCACATGGGTTTGGGTGGTGATGATAGCTGGTCTCCCTGTGTCCATGAGAAATACCTGATTCCAGCGGTGCCATACTCATTCT

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|169097332|gb|FE497150.1|FE497150

EST:     TGGATAGAGCAACTCATGAAGAAGAGCTGCATGCTGGACAGGACATTGAG                         GTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGT
genomic: TGGATAGAGCAACTCATGAAGAAGAGCTGCATGCTGGACAGGACATTGAGgtatccccca ... atacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGT

EST: gi|169024278|gb|FE435230.1|FE435230

EST:     TGGATAGAGCAACTCATGAAGAAGAGCTGAATGCTGGACAGGACATTGAG                         GTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGT
genomic: TGGATAGAGCAACTCATGAAGAAGAGCTGCATGCTGGACAGGACATTGAGgtatccccca ... atacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGT

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 1 RNA-Seqlibrary.

Block sizes: 35 (upstream exon), 20 (downstream exon)
Score: 7

AGGAAGTCCTCCAATGCAAATGAGTGCCAGCAACTACAGTACAGAGGAGCTGGATAGAGCAACTCATGAAGAAGAGCTGCATGCTGGACAGGACATTGAGgtatccccca ... atacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ccccagagctttcttttcaccttttgtttcttactgtttgttttaatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG