ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC

Basic information

species	Physcomitrella patens
transcript	PP1S66_174V6.1
intron #	13
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttg----ttttacttgttgcatgatgtctcacggtgtttatttc-tg--tagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                                             | ||| |  |||  |   || ||||| | |   | || |  | || |      ||    || |||   |   ||| |    || | |||  ||   ||| ||  | || || ||||| ||||| ||||| || || || ||||||||||||||||| || |||||||||  |||||| ||| | |||||| |||||||
---------------------------------------------------------------------------ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacagattagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 13

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
           | ||  ||||  ||| |||| |    |  || |   | ||   |    | || | |   ||  ||    ||| |   |  ||| |   | | |||   |  |||    | |  ||||| |  |||    | |  | |    |  || ||   | |||| ||   ||||  |||||| || || ||||| || || || |||||||||||||||||||| || |||||| ||||||| ||||| || ||| | |||||
-----------gtta--atcccctgaagtatttattcttcatgtattgtgtct-ttgggatggcgataattggcttgagtttagatgatcacatgttttg-cttttgcatattttgactggttatgtttaaactgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTGCAGCAATCCTATAAAGTCAGTGATTCATTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgat-ctcaagggtgtttgatgatttat-tcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                 ||| || | |  |    ||| ||  || || | || |   ||     | | |    | |   |  |||    | |  ||||| | ||||    | |  | |    |  || ||   | |||| ||   ||||   ||||| || || ||||| || || || |||||||||||||||||||| || |||||| ||||||| ||||| || ||| | |||||
-------------------------------------------------gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                                         ||  | | | |||  | |   ||||  |  |   | |||    |    |    ||||  ||   || |||      | | | ||    ||   ||| ||   |||   |||||| || || ||||| || ||||| ||||| || |||||||| || || || ||| | || |||||||||||||||||||||||
------------------------------------------------------------------------gttagtacctctaaagtatatattggcaatgtcaatttgg----caaatttcaattttgttttccgc-tgac----tatgatcttggactcc--agGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 13

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                                      | | ||  ||||| | | | | ||       ||| | |   ||||      | |   |||   ||||    | || || | | | ||    ||   ||| ||   |||   |||||| || |||||||| || || || ||||| ||||||||||| || || || ||| | || ||||||||||||||| |||||||
---------------------------------------------------------------------gttagttcctcttaaagtatat-atc-----gcctatgt-cagtttggcaattttcaattt---tgttttccgctgact-atgatcttggactcc--agGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                      ||| |||  || | |   || | || |     | |  | |       |  | ||     || ||  |||| |      |   |       |    |||    |  ||||||  ||   || |       | |||  |||   ||||||||||| || || ||||| ||||||||||| |||||||||||||| || |||||||| || |||||||||  |||||  ||  | || || || ||| |
---------------------gttggtgttaatggtagtaatctgcaaa-----tttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgct------tgttgtaaattg--gtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                      | || |   | ||| |||| |  || | |  | ||      |   |   ||||  | || |      |  ||  ||| |   ||  || | | |||      | | || || ||| |||  ||| || ||||||||||||||||| ||||| || || || || |||||||| || ||||||||| ||||||||||  | || || ||||||||
-----------------------------------------------------gtatctacact-tttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggt-tttcaaa----tgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                                  | | |  |    ||| || ||   |        || ||| |||    ||  |    | ||     | | || | |    |  |||    | || | |  |||||||  | || || ||||| ||||||||||| |||||||| |||||||| |||||||| ||||| || |||  |||||| ||| | || || || ||| |
-----------------------------------------------------------------gtcggtagtcacgtctcatgataactttgccaatgaacttattga---ttcataaagcatgaaagccgttttactta---ttccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 13

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataat--ttgtcatttggagaccttt-ttgtggttttctggctcttgtttt-acttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                                        |  ||||   || |      | |||  ||| ||    |||    ||| |||   || |||| |     |  || || |  |         || |||| ||| ||    || || || |||||||||||||| |||||||| ||||| ||||| ||||| || ||||| ||| ||||||| ||  | || ||||| |||||
------------------------------------------------------------------------acctatttacatgaagacactgattatgagtccccagttgctaatttatggtagttattttcagccactttatcatttgaccataaccaaatatctgcagGCACACAATATACTCAACAGTCTTACAAAGTAAGCGACTCCTTTCCCTTTAAATGGATAAACAAGAAGTGGAGAGAAGGATTCCATGTAACTTCCATGGC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 13

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttg--gagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                              ||   || ||| |||||  || ||    ||||||   |||||  |    |  |||| ||  | || | |  ||  ||   | |  |||     | ||  |   | |||| |||   ||    |||||||| || ||||| || || || ||||||||||||||||| ||||| |||||| |||| || || || || ||| | |||||
--------------------------------------------------------------gtcagtg-tgacttatt--taaaaccaatcattttttgagacaatgacttc-ttttatgattgttatctgtctcttt---taacctctgttaat-ttactgaatatagGCACGCAATATTTACAGCAGTCCTATAAAGTCAGTGAGTCATTTCCATTTAAGTGGATAAATAAAAAATGGAGAGAGGGTTTCTATGTTACTGCTATGGC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcat-ttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                  |   |||||      |||||| ||  | | | ||   ||||||| ||| | |   ||||| |      |||| | ||| ||      |  ||| ||| |     ||||||| |   |||||||  | || || |||||||| ||||||||||| || || ||||| ||||| ||||| |||||||| |||  |||||| ||  | || || || ||| |
--------------------------------------------------tcagtctcatccaaatttgatcatggaatttaat--cttgtcatgttgcatattgttttgag-----ttggcccatgtgtt------tatatggtgttttc---tgtttatgt---tagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgtt--ttacttgttgcatgatgtctcacg-gtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                                                                               || || | ||| || ||  |  |   | ||||  |  || ||| ||||||    | | ||| ||  | |||||||| || || |||||||||||||| || ||||| || ||||||||||| || || ||| | ||||| |||||||||||||| |||||
---------------------------------------------------------------------------------------------------------------gtattgtcgctgttattgatggccactggcattgtcgctgacgcgtgttt-cccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11

gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgtt--ttacttgttgcatgatgtctcacg-gtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
                                                                                                               || || | ||| || ||  |  |   | ||||  |  || ||| ||| ||    | | ||| ||  | |||||||| || || |||||||||||||| || ||||| || ||||||||||| || || ||| | ||||| |||||||||||||| |||||
---------------------------------------------------------------------------------------------------------------gtattgtcgctgttattgatggccactggcattgttgctgacgcgtgatt-cccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

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|162176121|gb|FC351889.1|FC351889

EST:     AATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG                         GAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTA
genomic: AATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAGgtattttatt ... atttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTA

EST: gi|162189086|gb|FC365204.1|FC365204

EST:     TGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG                         GAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTA
genomic: TGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAGgtattttatt ... atttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTA

EST: gi|162194954|gb|FC369032.1|FC369032

EST:     TGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG                         GAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTA
genomic: TGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAGgtattttatt ... atttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTA

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: 34 (upstream exon), 34 (downstream exon)
Score: 23

GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAGgtattttatt ... atttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC

<

<

<

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC

                               gtctcac  putative branch site (score: 23)
                                          tttatttct  putative PPT
                                        tgtttattt  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA