ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttcccatcttgagttattctgaagcttaacttttgatcgcaatgtgaccttaaagtttgaaatcttgaaggattttacgttcatcacattttgttatctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG

Basic information

species	Physcomitrella patens
transcript	PP1S10_201V6.1
intron #	12
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 12

---gttcccatcttgagttattctgaagcttaacttttgatcgcaatgtgaccttaaagtttgaaatcttgaaggattttacgttcatcacattttgttatctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG
    ||  |   |  | | |||    |  |     ||||| ||   ||   | | | ||||| ||  ||     ||||||      ||     ||| || ||  ||||||| || || || || ||||| ||||| |||||||| |||||||||||||||||||| || || |||||| | |||||||| ||  |  | ||||| || ||
tatatttgcccttaaaatgattaatgaattg----tttgaccgtg-tgctgcttgagagttttaacact-----gattttgataatatatttcttttttttcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12

gttcccatcttgagttattctgaagcttaacttttgatcgca-atgtgaccttaaagtttgaaatcttgaaggattttacgttcatcacattttgttatctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG
  ||  || ||   ||||  |||    ||| |||   | ||   ||   | | | ||||| ||  ||     ||||||  | | ||   ||| | || |   ||||||| || || || || ||||| || || |||||||| |||||||||||||||||||| || || |||||| | |||||||| ||  |  | ||||| || ||
-atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacact-----gatttt--gataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12

gttcccatcttgagttattctgaagctta-acttttgatcgcaatgtgaccttaaagtttgaaatcttgaaggattttacgttcatcacattttgttatctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG
             || ||  | | ||  | |  ||| || |  || |||   | ||         ||      |||||   ||  |    ||||  | |   || |||| || ||  | || || || || || |||||||| || ||||| ||||||||||| |||||||| || || |||||||| ||  | ||||||||||| ||
-------------gtaatgttcaggcacacagatttaatagttat-tga---tgaatcccattgcctatgctcatttttttttttttt--ttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG

upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12

gttcccatcttgagttattctgaagcttaacttttgatcgcaatgtgaccttaaagtttgaaatcttga-aggattttacgttcatcacattttgttatctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG
        | |||    ||  |  |  |    | | | |    ||| |||||    |   |  |  ||| | ||| ||       | | ||  |  |   | || ||||||| ||  | || || |||||||| |||||||| || ||||| ||||||||||| || ||||||||||| |||||||||||  |  ||||||| || ||
--------cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG

upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 12

gttcccatcttgagttattctgaagcttaacttttgatc--gcaatgtgaccttaaagtttgaaatcttg--aaggattttacgttcatcacattttgttatctgttg--cagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG
              ||    ||     |   ||||| |   ||||  |      ||  |||| |   ||    |  ||| |    | | |  || |  | ||    ||  ||||||| ||  | || || ||||| || || ||||| || ||||||||||||||||| || ||||||||||| ||||| |||||| |  | || || || ||
-------------tttccattggtagcttttttttggtgaagcaacatttttccaagttttgtatatttattcaaaattattttctaaaccaatgtgatcatggaatgttcagGTATCACAATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGG

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|100448629|gb|CJ972928.1|CJ972928

EST:     CAATACATCAAATATGCCTGTGGCTGCTCGTGAAGCTTCCATCTATACAG                         GTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGA
genomic: CAATACATCAAATATGCCTGTGGCTGCTCGTGAAGCTTCCATCTATACAGgttcccatct ... tctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGA

EST: gi|162165021|gb|FC342212.1|FC342212

EST:     CAATACATCAAATATGCCTGTGGCTGCTCGTGAAGCTTCCATCTATACAG                         GTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGA
genomic: CAATACATCAAATATGCCTGTGGCTGCTCGTGAAGCTTCCATCTATACAGgttcccatct ... tctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGA

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: 25 (upstream exon), 34 (downstream exon)
Score: 12

TTGCCTGACGGACGAGAGGAGTCTGTTATGAAGCGGACCACTCTCGTGGCCAATACATCAAATATGCCTGTGGCTGCTCGTGAAGCTTCCATCTATACAGgttcccatct ... tctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaagtttgaaatcttgaaggattttacgttcatcacattttgttatctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG