ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtttgtagtttacaaattgctgattttatcaccataagattattacatttcatccttttaccctggtatgggttctttgcttccgtcttgattgctttccatcttttttaatcagttgaagaggtaagaagtaatagtaggttgtttaatgcttgaagaaatgacctgcattgagtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA

Basic information

species	Physcomitrella patens
transcript	PP1S203_55V6.1
intron #	18
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 18

gtttgtagtttacaaattgctgattttatcaccataagattattacatttcatccttttaccctggtatgggttctttgcttccgtcttgattgctttccatct-tttttaatcagttgaagaggtaagaagtaatagtaggttgtttaatgcttgaagaaatgacctgcattgagtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA
                  |   ||||||  ||  |      | ||  ||   ||   ||    || ||    |    || |    |  | || | |||  ||   |   | ||   ||| | |  |||  ||||  |  | ||| |||   |  |||  |  ||  |   |||||       ||| |||||| || || |||||||| |||||||| ||||||||||| || |||||| |||| ||||| ||| | ||||| ||||  |||||||| || ||||
------------------gtaaattttaa-actgttgtgacactagtttctgtctggtt---ttgttaaatttcaactgttgtgctgcttatcgttttggatgaataactgattttttgtatatataatgagta-caccatgttcttttg-gaatgataagttgttccttattga------tagCATGAAGAAGGTGCTATTGAGGAAAGAGCTCGTGACTACAATGCAAATTGGATGTCAGCCGTTGAAATTGTTGATGATGACATATATCTAGGTGCAGAAA

upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 18

gtttgtagtttacaaattgctgattttatcaccataagattattacatttcatccttttaccctggtatgggttctttgcttccgtcttgattgctttccatcttttttaatcagttgaagaggtaagaagtaat-agtaggttgtttaatgcttgaagaaatgacctgcattgagtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA
                            | |   | | | | ||      |    || |  | |||| | | |   || |  | ||  |   |||||    | ||   | |  |  |||       | |  |||| ||||  || |||      || |   || |  ||   |      |  ||| |||||| || || |||||||| |||||||| ||||||||||| || |||||| |||| ||||| ||  | ||||| ||||  || ||||| || ||||
---------------------------gtaaattttaaactgttgtgacactagtttctgtc-tggttttgttaaatttcaactgttctt-ctgcttagtgttttggatgaataactgatttttgtatatataatgagtacattcttt------tggaatgataaattgttcttttattgatagCATGAAGAAGGTGCTATTGAGGAAAGAGCTCGTGACTACAATGCAAATTGGATGTCAGCCGTTGAAATCGTTGATGATGACATATACCTAGGTGCAGAAA

upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 6

gtttgtagtttacaaattgctgattttatcaccataagattattacatttcatccttttaccctggtatgggttctttgcttccgtcttgattgctttccatcttttttaatcagttgaagaggtaagaagtaat-agtaggttgtttaatgcttgaagaaatgacctgcattgagtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA
                            | |   | | | | ||      |     | |  | |||| | | |   || |  | ||  |   |||||    | ||   | |  |  |||       | |  |||| ||||  || |||   |  |||  || ||  ||  |||||       ||| |||||| || || |||||||| |||||||| ||||||||||| || |||||| |||| ||||| ||  | ||||| ||||  || ||||         
---------------------------gtaaattttaaactgttgtgacactagtctctgtc-tggttttgttaaatttcaactgttctt-ctgcttagtgttttggatgaataactgatttttgtatatataatgagtacattcttttg-gaatgataaattgttctttattga------tagCATGAAGAAGGTGCTATTGAGGAAAGAGCTCGTGACTACAATGCAAATTGGATGTCAGCCGTTGAAATCGTTGATGATGACATATACCTAG---------

upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 18

gtttgtagtttacaaattgctgattttatcaccataagattattacatttcatccttttaccctggtatgggttctttgcttccgtcttgattgctttccatcttttttaatcagttgaagaggtaagaagtaatagtaggttgtttaatgcttgaagaaatgacctgcattgagtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA
                                               |   |   |||      |  || | || |  |  |   | | || | | | |||  | ||  | |  |||        ||||| | |  | |   | ||              || | |||  ||   |     |||  || || || ||||| |||||||||||||| ||||| ||||| ||||||||||| || |||||||| ||  |||| ||||  || || ||  | || |
----------------------------------------------gtaaaacgttttggatacgaaattgtttttccgtctttatat-gaatacatgccaaatcttagatt--gttatgttcacaagaactcaccggactctttt-------------gattatctgtgtttgttttaa-agCACGAGGAAGGTGCGATCGAGGAGAGAGCTCGGGACTATAATGCAAACTGGATGACGGCAGTTGAGATACTCAATGATGACATCTACCTCGGTACTGATA

upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18

gtttgtagtttacaaattgctgattttatcaccataagattattacatttcatccttttaccctggtatgggttctttgcttccgtcttgattgctttccatcttttttaatcagttgaagaggtaagaagtaatagtaggttgtttaatgcttgaagaaatgacctgca-ttgagtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA
                                                                                          ||  |||     |    ||  |  ||| || |  | |      ||    | |  |||  |  |       ||| | |    |||| |     |||  || || || || ||||||||| | ||||| || |||||||| || |||||| ||||||||||||| || ||||| || | ||| || || || || |
----------------------------------------------------------------------------------------gtataacttctagacgaaatttgtgtgtttaaaaactgatctactat----gttcatttggtattgtttctgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA

upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 18

gtttgtagtttacaaattgctgattttatcaccataagattattacatttcatccttttaccctggtatgggttctttgcttccgtcttgattgctttccatcttttttaatcagttgaagaggtaagaagtaatagtaggttgtttaatgcttgaagaaatgacctgcattgagtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA
                                  |||||| | ||   ||||     |  |||| ||        ||||    |   |     | |  |     ||   |    ||||     ||  |      |  | |  |  ||||||  ||    | ||  |    ||   |    |||| ||| || || || ||||| ||| |||| || ||||||||||| || |||||| |||| ||||||||||| ||||| |||| ||| || || || || |
---------------------------------gtaagatgactaatcttcaagtaat--cccttgt-----ccttttggcagcaagtatggcgttccctggagttaaaagagtgttgtgtttgtttgttactcttatcgtcttgttaatggatgtctgattggtcctttttttatttt-cagCATGAGGAAGGTGCCATTGAAGAGCGAGCCCGTGACTACAATGCAAATTGGATGTCAGCTGTTGAGATTCTTGATGATGACATTTACCTTGGTGCTGAGA

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|162207422|gb|FC383979.1|FC383979

EST:     TTATCGTTGTGGGAGATCTGATGAAGTCAATTTCGCTTCTCATTTACAAG                         CCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGG
genomic: TTATCGTTGTGGGAGATCTGATGAAGTCAATTTCGCTTCTCATTTACAAGgtttgtagtt ... agtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGG

EST: gi|162257635|gb|FC433562.1|FC433562

EST:     TNATCGTTGTGGGAGATCTGATGAAGTCAATTTCGCTTCTCATTTACAAG                         CCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGG
genomic: TTATCGTTGTGGGAGATCTGATGAAGTCAATTTCGCTTCTCATTTACAAGgtttgtagtt ... agtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGG

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: 33 (upstream exon), 15 (downstream exon)
Score: 4

TTCCCACCATGGGCATATATTGGCATTGTATGTTCAATCACGAGGAGATTTTATCGTTGTGGGAGATCTGATGAAGTCAATTTCGCTTCTCATTTACAAGgtttgtagtt ... agtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aagtaatagtaggttgtttaatgcttgaagaaatgacctgcattgagtccggcagCCTGAAGAGGGAGCGATTGAGGAGAGAGCTCGAGACTACAATGCCAACTGGATGACAGCGGTTGAGATTCTGGATGACGACACTTATCTAGGGGCGGAAA