ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagttactattcctgatgtcaccgatcgattgcgcgtacctgatctcatatgctgtattttaaattctacaaagatttcgaggatgctaacatgccgtacttgcatcacaccatgttccactgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCTGCACCGGACGAAGGCGACGATAATTGGTTTGTTTGACATCGGTAACGTG

Basic information

species	Physcomitrella patens
transcript	PP1S36_214V6.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S36_214V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA19G37480.1 (Glycine max), 3'ss of exon 7

gtaagttactattcctgatgtcaccgatcgattgcgcgtacctgatctcatatgctgta-ttttaaattctacaaagatttcgaggatgctaacatgccgtacttgcatcacaccatgttccactgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCTGCACCGGACGAAGGCGACGATAATTGGTTTGTTTGACATCGGTAACGTG
            || |||| || |       |||| |     | |  ||| ||| |  | |||||||  | |  ||  | |   | | |  |   |    |   |  ||  ||   ||||   || |||  ||||||||| || ||  |||| ||||||||||| || |||||||| ||||| ||||| || || ||||| ||||| ||||||||  ||||     ||   |||
-----------gtcttgatttctcttgagttttgctctattatcaaatcacatgatccaattttaaagacaaggaacttgttttgcaagtaagagtttgttgactttatt-cattgtgtttt-ctatgtttcagGTCACTCCATTTGATGGTCTTCTGGATTCTCTTTGAGAATGTCATGTCTCTGCATCGAACAAAGGCAACGATTATTGGTTTACTTGAGGCAAGTCGAGTG

upper sequence: PP1S36_214V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 7

gtaagttactattcctgatgtcaccgatcgattgcgcgtacctgatctcatatgctgtattttaaattctacaaagatttcgaggatgctaacatgccgtacttgcatcacaccatgttcc--actgtgtc--acagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCTGCACCGGACGAAGGCGACGATAATTGGTTTGTTTGACATCGGTAACGTG
                           ||  || |  ||| || |  ||||   || | |||    ||  | |  | || |    |||  |     | |   ||  |||      | || |  | | |||   | |||||| | ||  |  || | |  |||||||| ||||||||||||||||||||||||||||| ||||| ||  | |||||| |||||||    || |  |  
---------------------gtatattctgttccttgtatctcaagtcattatctctgtttc---tttcataggg-ttgcttatatgtcacgtaactgagtttaaatccttttctatttctgattttgttcaaaagGTCAATTCATCTGCTGTTCTATTGGATTCTATTCGAGAATGTGATGTCGCTGCACCGGACAAAGGCCACTCTCATTGGTCTGTTTGAGGCAGGAAGGGCT

upper sequence: PP1S36_214V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv08s0007g03990.t01 (Vitis vinifera), 3'ss of exon 7

gtaagttactattcctgatgtcaccgatcgattg-cgcgtacctgatctcatatgctgtattttaaattctacaaagatttcgaggatgctaacatgccgtacttgcatcacaccatgttccactgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCTGCACCGGACGAAGGCGACGATAATTGGTTTGTTTGACATCGGTAACGTG
                               ||| | |  | | || |   |  | || | || || ||     |    ||       | |   || ||    |    || |   |  ||    | | |  ||||||||| |||||| ||||||||||||| || || |||||||| ||||| || || ||||| ||||| ||  | |||||  || | ||   |||||  || 
-----------------------------agttgtcccaaaacagacccacttggttgcagttcaactttctggattgctttcccatggtttctattcc----tcatgtcgcttta-attaatgtatctttcagGTCACTCCACTTAATGGTTTTCTGGATCCTTTTTGAGAATGTCATGTCCCTACATCGGACCAAGGCTACCTTCATTGGACTGCTGGAAGGCGGTAGAGTT

upper sequence: PP1S36_214V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv13s0074g00500.t01 (Vitis vinifera), 3'ss of exon 7

gtaagttactattcctgatgtcaccgatcgattgcgcgtacctgatctc-atatgctgtattttaaattctacaaagatttcgaggatgctaacatgccgtacttgcatcacaccatgttccactgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCTGCACCGGACGAAGGCGACGATAATTGGTTTGTTTGACATCGGTAACGTG
                            | | || || |    ||| |  | ||  || | || || ||         || |       || |  |    |||||     |    ||||   |   | |  ||| ||||| ||| | |||||||||||||| || || |||||||| ||||| |||||||| || ||||||||  | || ||| |  | ||  | || |  || 
---------------------------gcaaatgggctt--tagatttggaaataatgcaattgaattttcctcccttttactcattaacttatttctgatacttttg--aatgtatgt---atgatcttgcagATCACTCCACCTCTTGGTTTTCTGGATACTTTTTGAGAATGTCATGTCCCTGCACCGAACTAAGGCGACATTCATGGGTCTCCTAGAGGTGGGGAGAGTA

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|162201162|gb|FC377669.1|FC377669

EST:     GTGTACGTTCCGTCGATCATCACTCTGCTCAATGCCATCACCACCCCCAA                         GTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCT
genomic: GTGTACGTTCCGTCGATCATCACTCTGCTCAATGCCATCACCACCCCCAAgtaagttact ... tgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCT

EST: gi|208368302|gb|DC955513.1|DC955513

EST:     GTGTACGTTCCGTCGATCATCACTCTGCTCAATGCCATCACCACCCCCAA                         GTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCT
genomic: GTGTACGTTCCGTCGATCATCACTCTGCTCAATGCCATCACCACCCCCAAgtaagttact ... tgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCT

EST: gi|208393449|gb|DC942519.1|DC942519

EST:     GTGTACGTTCCGTCGATCATCACTCTGCTCAATGCCATCACCACCCCCAA                         GTCACTGCACTTATTGGTTTTCTGGATTCTGTTCNANAATGTGATGTCCCT
genomic: GTGTACGTTCCGTCGATCATCACTCTGCTCAATGCCATCACCACCCCCAAgtaagttact ... tgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCT

EST: gi|162198830|gb|FC374313.1|FC374313

EST:     GTGTACGTTCCGTCGATCATCACTCTGCTCAATGCCATCACCACCCCCAA                         GTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCT
genomic: GTGTACGTTCCGTCGATCATCACTCTGCTCAATGCCATCACCACCCCCAAgtaagttact ... tgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCT

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: 30 (upstream exon), 26 (downstream exon)
Score: 7

TCCCTGCCTCGGTGTTGGTCCCCGAGGTCGACCTTCCATTCTGGGGGGCTGTGTACGTTCCGTCGATCATCACTCTGCTCAATGCCATCACCACCCCCAAgtaagttact ... tgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCTGCACCGGACGAAGGCGACGATAATTGGTTTGTTTGACATCGGTAACGTG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcgaggatgctaacatgccgtacttgcatcacaccatgttccactgtgtcacagGTCACTGCACTTATTGGTTTTCTGGATTCTGTTCGAGAATGTGATGTCGCTGCACCGGACGAAGGCGACGATAATTGGTTTGTTTGACATCGGTAACGTG