ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA

Basic information

species	Selaginella moellendorffii
transcript	EFJ28117
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 11

---------gtaagc---gtttgctttgcatgatacttgaaacgc---------tcatga------gtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
         | |  |   || ||||  ||| || |   |||| |           |||||      ||  ||   | |  ||||||||||| |||||| | || |||||||| || || || || ||||||||||| ||||| ||||| ||||| || |||||    ||| | ||  | ||  
gtatatcgtgcatactaggtgtgctaagcaggaaagaagaaatgagaaaaaaaaccatgatatattgttgctgcatttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 16

-----------------------------------gtaagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                                   || |       | |     | |  || |     |  || ||    | |  |  ||||| || || || || ||  | ||| |||| || ||||||||| |||||||||| ||||| ||||||||||| || ||| |  ||||||||||||| ||  
gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA07G03930.2 (Glycine max), 3'ss of exon 16

-----------------------------------gtaagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                                   || |       | |     | |  || |     |  ||  |    | |  |  ||||| || || || || || || ||| |||| || ||||||||| ||| |||||| ||||| ||||||||||| || ||| |  ||||||||||||| ||  
gtaattggagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttggcttgaattgcattacagGGAGGTACATTTACAGTGTCTAACCTGGGAGGGCCATTTGGTGTCAGACAATTCTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGAT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16

------------------------------gtaagcgtttgcttt--gcatgatacttgaaacgctcatgagtcccttggtgt-cgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                               |    | ||| ||    |||| |  || ||| |  | | |    | |  | |  |||||| ||||| || || || ||||||||||| |||||||||||  |||||||||||||||| || |||||||| || || ||  |||| || || || ||  
gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17

---------------------------------gtaagcgtttgctttg-catgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                                 | ||| | | |||  |   | | |  |||||      |  ||||       | |||||| || || || || || || ||  |||| ||||| ||||||||||| ||||| ||||| ||||||||||| || |||||  ||||||| ||| | ||  
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctcc----ttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: PP1S78_56V6.1 (Physcomitrella patens), 3'ss of exon 14

---------------------------------------------gtaagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                                              |     ||| ||| |  |  ||||  |     |  | | | |     |   ||||||||| || || ||  |||| || ||||| ||||| ||||| || |||||||||||||||||||||||||| || ||  |   ||||||||| || || |
attccgtgtttctgtgatttgaagattatgatttttattttttagtttcatttttccttcgttttttactaaatgttttt-taactgcaacaattctgcagGGTGGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGA

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|169037977|gb|FE446627.1|FE446627

EST:     CGTTGGCGGAGAAGGCTAGGGAGAACACACTGAAGCCTAGTGACTACGAT                         GGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAA
genomic: CGTTGGCGGAGAAGGCTAGGGAGAACACACTGAAGCCTAGTGACTACGATgtaagcgttt ... ggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAA

EST: gi|169109080|gb|FE511282.1|FE511282

EST:     CGTTGGCGGAGAAGGCTAGGGAGAACACACTGAAGCCTAGTGACTACGAT                         GGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAA
genomic: CGTTGGCGGAGAAGGCTAGGGAGAACACACTGAAGCCTAGTGACTACGATgtaagcgttt ... ggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAA

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), 34 (downstream exon)
Score: 71

GATGCTGATAAGAAAGGGTTGGGAGCTATTTCGGACGATGTAAGAACGTTGGCGGAGAAGGCTAGGGAGAACACACTGAAGCCTAGTGACTACGATgtaagcgttt ... ggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA