ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...tttgttttattccatagcttaacccttagttcttcaatagcgcggttaaacgctagttgaatatttcacagttgttgattgcttgagagctcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGAAGGGCAAGGTTCCCGTGTCTCTCGACCACCTCAGTATCCGTGGCAATAA

Basic information

species	Physcomitrella patens
transcript	PP1S726_1V6.1
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S726_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 3'ss of exon 2

-------tttgttttattccat---agcttaacccttagttcttcaatagcgcggttaaacgctagttgaatatttcacagttgttgattgcttgagagctcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGAAGGGCAAGGTTCCCGTGTCTCTCGACCACCTCAGTATCCGTGGCAATAA
       | |   ||  | |||    | | |    ||  |   |  | |  || ||||    || |   ||| |||||    |  |||||  |  |     ||||||||||||||||||| |||||||||||||| |||||| |||| ||||| ||  |||| || ||   ||| ||  | || |||||||||||| |  | || || ||
tcatgtttctagctttcttcatgttggttgaggtgtttttaggtggacaaggctgttatgtcctgg---aatgtttcaa---ttctgattcatcaa----ccttttgcagGTGTGGATATAAGCATGAACACCCACTTGAAGACTGTTAAGCTCACATTGAAAGGGAAAAATCCTGTAACCCTTGACCACCTCAGTGTGAGAGGAAACAA

upper sequence: PP1S726_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3

tttgttttattccat--agcttaacccttagttcttca-atagcgcggttaaacgctagttgaatatttcacagt---tgttgattgcttgagagctcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGAAGGGCAAGGTTCCCGTGTCTCTCGACCACCTCAGTATCCGTGGCAATAA
||| |   || ||||  |  ||  | |  | | | ||| ||    | || || |      ||| ||||    |||   |  |||||  |||        |||| |||||| || ||||||||||| || ||| ||||| ||||||||||||| || || || ||   ||| ||  | || || ||||| ||| |  | || || ||
tttttaacatcccattaaaattctctcccattccatcagattttacagt-aatcctagaatgattattcagtagtgtattctgattttttgga-----ctttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA

upper sequence: PP1S726_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 2

tttgttttattccatagcttaacccttagttcttcaatagc----gcggttaaacgctagttgaatatttcacagttgttg--attgcttgagagctcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGAAGGGCAAGGTTCCCGTGTCTCTCGACCACCTCAGTATCCGTGGCAATAA
   ||    |    ||| | |  || |  |    ||| | |      |  | || | |  ||| | |  |||  | || ||  |||||||   |    | ||  |||||||||||| || |||||||| ||||||||| ||||||| |||||||||||||| ||   ||| ||| || | || ||||| ||| |  | ||||| ||
--agtaacttgaagtaggtaagtccatgttatgacaaaaactatttagaatcaaagatgattggagagatcattgctgatggtattgctttgta----tgttatagGTGTGGATATTAGTATGAACACACATTTGAAGACTGTGAAACTGACTCTGAAGGGGAAAAATCCAGTGACTATGGATCACCTGAGTGTGAGGGGCAACAA

upper sequence: PP1S726_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ08912 (Selaginella moellendorffii), 3'ss of exon 2

tttgttttattccatagcttaacccttagttcttcaatagcgcggttaaacgctagttgaatatttcacagttgttgattgcttgagagctcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGAAGGGCAAGGTTCCCGTGTCTCTCGACCACCTCAGTATCCGTGGCAATAA
                              | |    |  |  || ||    ||||       |||| | | |     |  |||     ||  | || ||| |||||||||||||||||||||||| | ||| | |||||||||    |||| || |||   |||||  |  | || || ||||| ||||| || || ||
-----------------------------gtgtgatgtctctaggctagtttctagcgattgttttctctgataagtttcccttttcctctggtgtgtagGCGTGGATATCAGCATGAACACCCATCTCAAGGCCGTGAAGCTGGTGTTGAAAGGGAAGAACCCCGTCACAATGGATCATCTCAGCATCCGAGGGAACAA

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|19778390|gb|BQ039306.1|BQ039306

EST:     GGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG                         GTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA
genomic: GGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAGgtatgtagtt ... tcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA

EST: gi|19786461|gb|BQ040480.1|BQ040480

EST:     GGGATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG                         GTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA
genomic: GGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAGgtatgtagtt ... tcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA

EST: gi|18327020|gb|BJ159021.1|BJ159021

EST:     GGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG                         GTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA
genomic: GGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAGgtatgtagtt ... tcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA

EST: gi|19777854|gb|BQ039234.1|BQ039234

EST:     GGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG                         GTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA
genomic: GGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAGgtatgtagtt ... tcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA

EST: gi|67575738|gb|BJ948562.1|BJ948562

EST:     GGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG                         GTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA
genomic: GGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAGgtatgtagtt ... tcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGA

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: 13 (upstream exon), 23 (downstream exon)
Score: 1

ATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAGgtatgtagtt ... tcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGAAGGGCAAGGTTCCCGTGTCTCTCGACCACCTCAGTATCCGTGGCAATAA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttaaacgctagttgaatatttcacagttgttgattgcttgagagctcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGAAGGGCAAGGTTCCCGTGTCTCTCGACCACCTCAGTATCCGTGGCAATAA