ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG

Basic information

species	Physcomitrella patens
transcript	PP1S85_75V6.1
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 9

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG
                                                                       ||||  ||||  | | || |   |   | |||  || |   |  |    |  | | ||   | | ||     || ||   ||    |   |  |    | | ||||||||||||||||| || ||||||||||| || ||||| ||||||||||| ||||| || ||| | || ||||| || || |||||||| || || || |
-----------------------------------------------------------------------aaat-ctagtccttttaataccacggtt-tatgctgatttcttaagtattatatcatt--caagtcacctctacttaccttttctctgtctttcctcac-atcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTATATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG
                                                      | | ||| |   ||||    | |  |   | |||||| |  |    |||||||       | ||  ||               | ||||  |    ||  ||| || |       |    |||| ||||| || || ||||||||||||||  | ||||| || || ||||||||||| || |||||||| || || ||||||||||||||  |||||||||
----------------------------------------------------catttatttatctctttt----tctccg-actataaaaagtaactaagtattttgcaaacaattagattg---------------acaatggaa----ctattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 9

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctt-tagtatgccagaatgaca-tattcttatgatccttaactatg-cgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG
                                                                                |||  | | |  |    ||| |   | || |   |||    | |  ||  |       ||| ||||| |     ||| | ||    ||    |    |||| ||||| || || ||||||||||||||  | ||||| ||||| || |||||||| || |||||||| || || ||||||||||||||  |||||||||
------------------------------------------------------------------------------catgtatttatatctttttctc-agagtattagaagtaacaaagtattttgcaaacaattagattgacaatggaactattaaccccttctggatcttgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTATCCCGGCTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 9

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacct-ttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG
                                                                      | ||  | | | ||  | |         |   |||  ||  | | | || |   ||| ||  | |   | ||| | ||     |  ||     |||| |      ||||||| || || || ||||| || || ||  | ||||||||||| ||||| |||||||| |||||||| |||||||| |||||||||||||| || || |
----------------------------------------------------------------------gtaaaatgaatatttgataccggagtagttcctttatttcataccatgttttttcctcttcatgtttgataataagat-----tgaga-----aactgt------agGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttg--gttctaagtctgcacctttagtatgccagaatgacatattctta-tgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG
                                                                                     |||  | |  | || |  |||||    || | | |  |  |  |||  | |   ||  |   |||   |||   | | | |||| |      |||||||||| ||||| |||||||| |||||  | ||||||||||| || || ||||| || |||||||| |||||||| ||||| || || || ||||| |
------------------------------------------------------------------------------------gtaatgagtttcactgtcctttgtgtatgtcccatgattcaaaatttgattta--agctttgaataaaattaacaaacgtgaactct------agGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 9

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG
                                                          ||  | | |||| ||||  ||     |  | ||  |    ||||||       | | |    | |   |||    | |  || ||  | ||   | |     || |||       ||||| |||||||| || || |||||||||||  | ||||| |||||||| || ||||| || |||||||| || ||||| || |||||||| || || || |
---------------------------------------------------------cttcataggttttaaaatcata-----cggataatcgaatttctattgcaccattcccacacttac---tttcacctacttgactggaa-atgtctgt----tttgactg------cagGTATCTGCAGCCCGGGAGGAAGTACCTGGAAGGCGTGGGTATCCTGGGTATATGTATACTGATCTTGCAACAATTTATGAGCGTGCTGGACGTATAGAAG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG
                                              ||||| | | |||| |||  | ||            ||  |  || | ||||  |   || ||    || |      |   ||   ||||   ||  || ||||            ||||       ||||| ||||| || || |||||||| || ||| | ||||| |||||||| || ||||| || ||||| || || ||||| ||||||||||| || ||||| |
----------------------------------------------cttctaattttgttcttgagtatt------------tttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgc--aaactacttattgc----------aactg------cagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG
                                                                                                                  || |  |     |  ||| || ||  |   |       ||||||    |    |  |   |||| ||||| |||||||| || || ||||| |||||||||||||||||||| ||||| || ||| | || || |||||||| |||||||| |||||||| |
-----------------------------------------------------------------------------------------------------------------gtatgg-tatgtttcaagtttgtcatgagagc-------tatgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 8

gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG
                                                                                                                | | |   |     |  ||| |  ||   ||| |  || | || | || |  || || |   |||| ||||| |||||||| || || ||||| |||||||||||||||||||| ||||| || ||| | || || |||||||| |||||||| |||||||| |
---------------------------------------------------------------------------------------------------------------gtatgatcgtatgtttcaagtttttca---tgaga-gttatgataa-ccatggctttgtg--tagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

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|100417322|gb|BY957275.1|BY957275

EST:     TTCTGGTCATCCTGACGGATATGAGTTCATACGCAGATGCATTGCGTGAG                         GTTTCTGCAACTCGTGAAAGA-GTACCTGGGCGTCGTGGATATCCTGGNTA
genomic: TTCTGGTCATCCTGACGGATATGAGTTCATACGCAGATGCATTGCGTGAGgtaccagtct ... atgcgaacagGTTTCTGCAGCTCGTGAA-GAAGTACCTGGGCGTCGTGGATATCCTGGTTA

EST: gi|162190700|gb|FC367586.1|FC367586

EST:     TTCTGGTCATCCTGACGGATATGAGTTCATACGCAGATGCATTGCGTGAG                         GTTTCTGCAGCTCGTG
genomic: TTCTGGTCATCCTGACGGATATGAGTTCATACGCAGATGCATTGCGTGAGgtaccagtct ... atgcgaacagGTTTCTGCAGCTCGTG

EST: gi|162274941|gb|FC450592.1|FC450592

EST:     TTCTGGTCATCCTGACGGATATGAGTTCATACGCAGATGCATTGCGTGAG                         GTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTAC
genomic: TTCTGGTCATCCTGACGGATATGAGTTCATACGCAGATGCATTGCGTGAGgtaccagtct ... atgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTAC

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: 35 (upstream exon), 35 (downstream exon)
Score: 11

AATTGCACTTACAACTGCTGAGTACTACGCTTATGAGTGTGGAAAGCACGTTCTGGTCATCCTGACGGATATGAGTTCATACGCAGATGCATTGCGTGAGgtaccagtct ... atgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG