ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacgaagattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA

Basic information

species	Physcomitrella patens
transcript	PP1S9_103V6.1
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8

gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacga-agattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
                                      |  ||   ||||  |||   | |    | |  | |   | || | |    | |||   || |      | ||  |||   ||  |  |       || |   |||| |||||||  || |  ||| |||| ||||| ||  | ||||| |||||||| ||||||||||| || || ||  | ||||||||||||||||| ||||
-------------------------------------gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatattt--atgagtttatctctaatacctttac---agGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8

gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacgaagattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttcct---tagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
                                      |  |||||||    ||  |||  | ||       |||| | |||    |||  |||   ||  | |   ||   |    |||   ||| | |   |   |    ||||  |||||| |||||  ||  | ||||| || || || ||||| |||||||| ||||||||||||||||| ||| | |||||||| ||||||||||| |
-------------------------------------catgatctgtt----tgtgcttgattattaagcccttatatcctt---gaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 8

gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacgaagattatctgctttggaaacaatctcaattacttccagtttgatggact-tgccagtgtcgtgg-tttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
                                         |||||||    ||  |||  | ||       |||| | |||         | |   |||||    || ||    | | ||   |  |  |   |||    ||||  |||||| |||||  ||| | ||||| || || || ||||| ||||| || ||||||||||||||||| ||| | |||||||| ||||||||||| |
---------------------------------------ttatctgtt----tgtgcttgattattaagcccttatatccttgaatcttctttttttttactgggtgtgtgtaacattatgtgtgccttttaactttgaacagGTGACTGCTGCAAAGGCAGACTTAAATTATATTGGGTTAGATGGAGAAATAGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 8

--------gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactt---tgtaatacgaagattatctgctt-tggaaacaatctcaa---ttacttccagtttgatggact-tgccagtgtcgtggtttcctt-------agGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
          || || || |   |||    || || | | ||  ||   |  ||   |   |||| |     ||  |  |||   |||  | | |    ||||   |||     |  |  ||    ||      ||      | ||||||||  |       |||| |||||||  || |  ||  |||| ||||| || || ||||| |||||||| |||||||||||||| || ||  | ||||||||||| |||||||| |
gttgggttacttctttta-atttcttgaccctgttttatctgtgatg-taagtggaaagtagcacatgtacataccataaaggcaatccccctctcttcacaactacaaggtaaaactaaagaacaatatgtaatgttctatttgtggtttcactgtacaatagGTGGCTGCTGCCAAAGCAGATTTGAACTACATCGGCTTAGATGGAGAAATTGGTTGCATGGTGAATGGTGCTGGCTTAGCAATGGCTACCATGGATATAA

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ13492 (Selaginella moellendorffii), 3'ss of exon 8

gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacgaagattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA
                                                                                 || || ||  | |  ||   |||  |||| |      |||| || |||          |||| |||||||     |  ||  |||| ||||| ||||||||||| || ||||| ||||||||||||||||| || || || ||||| || ||||||||||
--------------------------------------------------------------------------------gtttgagaccttgttcatagtttcacgttttaa-----tgcctgt-tcgaaaaac----agGTCGCTGCTGCTGCCGCCGATTTGAACTACATTGGATTGGATGGCGAGATTGGCTGCATGGTGAATGGAGCAGGACTCGCGATGGCAACCATGGATATCA

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|208362322|gb|DC954568.1|DC954568

EST:     AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT

EST: gi|208364988|gb|DC947130.1|DC947130

EST:     AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: AAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT

EST: gi|208371603|gb|DC952245.1|DC952245

EST:     GCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: GCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT

EST: gi|208364115|gb|DC950407.1|DC950407

EST:     ATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAG                         GTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT
genomic: ATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATT

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: 31 (upstream exon), 29 (downstream exon)
Score: 10

GATGGCCGCCGACGCGAAGCTTAACTTTGATGACAATGCAGCCTTCCGTCAAAAGGAAATCTTTGCCATGCGAGACACAACACAGGAAGACCCTCGTGAGgtttgttgta ... gtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttccttagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA