ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT

Basic information

species	Physcomitrella patens
transcript	PP1S2_667V6.2
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 3'ss of exon 6

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgattt-cacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
                              |   | | |   || ||   ||  |    ||     |||   |||| |  | |  || || || | |  |||   | || |||   |  ||||| || |||||||||||  ||||||||||| | |||||||| || || |||||||| |||||||||||  | ||| | |
-----------------------gtttgccaccttgaatctcacttgttctgcttttactgtgtcaattggtaccttac-agtcttggtgtttgtat-cagGGTTTGGGTAAGCATGACATCATCTGCATTGAGGATCTTGTTCATGAGATCATGACTGTTGGCCCACATTTCAAGGAGGCCAACAACTTCCTCTGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G094051_T05 (Zea mays), 3'ss of exon 5

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctg----ttgattttgtgtagGCACTTGGA-AAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
  || |  | |  || |   | |||    |    ||  |  |  |||   | |||   |  || |    | || ||||||  ||      ||| | || | |  |  |||||  |||      ||||| || |||||||||||  |||| |||||| | |||||||| || ||||||||||| |||||||||||  | ||| | |
--gtttgtaaacttggaactctaca----tctggttcctgtgttctg---tttatatatgacaat----ttacatgatgatctccaccttttggtgttctatcagGGCTTGGGCAAGCACAACATCATCTGCATTGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 6

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctg----ttgattttgtgtagGCACTTGGA-AAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
  || |  |    ||   |  |   ||  |  |     |  || ||| | |||||  ||  || |    | || ||||||  ||      ||| | || | |  |  |||||  |||      ||||| || |||||||||||  ||||||||||| | ||||| || || ||||||||||| || ||||||||  | ||| | |
--gtttgcaatcttgagctctg---cacctggatcctttgtgatctg-cttgtat--ttgacaat----ttacatgatgatctccaccatttggtgttctatcagGGCTTGGGCAAGCACAACATCATTTGCATTGAGGATCTTGTTCATGAGATCATGACTGTCGGCCCACACTTCAAGGAGGCGAACAACTTCCTTTGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA15G18170.1 (Glycine max), 3'ss of exon 6

--tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
   ||| |       |   | |   | |  | || | |   |   | ||     | |  |    |||  |||  |||||   |   | |  ||       || |  | || |||   || ||||| ||  |||| ||||| || ||||||||| | ||||||||||||||||||||||| |||||||| ||| | ||| |||
gtccgtgtggtctattctgtagtc-ctctgtaaacacttccattgcttgtttgttctattacttagtttttttccctgacataacat-tcaatgcc----agACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATCATGACTGTTGGACCTCACTTCAAGGAGGCCAACAATTTTCTGTGGCCTT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 6

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttg--tgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
                        |   || |  |||  |    ||  | |  |   |||  | | | ||| |   |||  |  |  |   || |     |||| || || ||||  || |||||||  | ||| ||||| || ||||||||| ||||||||||||||||||| ||||| || ||||||||  | ||| | |
----------------------gtattgtttattttacaat--tcttccttacagatttt--aattaattcgctacatgcttcttacttgcttggatgacagGCTCTGGGCAAGTATGGAATCATATCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGACCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatga-attctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
  || |   | |       || |  ||  |  || ||     |      || | | || |  | | | ||     | ||| ||    || | |      || |  | || |||   || ||||| ||  |||| ||||| || |||||||| || |||||||||||||| |||||||| |||||||| ||| | ||| |||
--gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctat-tactcagttttttcgctgacataacattcaatgc---cagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6

-----------------------------------------------------------------------------------------tcgtataaatagctgcattgcgacacaattaa---aattagtaggacctgacgtgtatcctttgca----gtgatttcacctgatgaat---tctgttgattttgtgt-agGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
                                                                                           |||| |  | |    ||| ||  |||||     ||    || |   || | | |||| |    |     ||  ||| |   ||  |    ||  ||| | |||  | |||  || ||||||   || ||||| ||  |||||||||| || ||||||||| | || ||||| || || |||||||||||||| |||||||| ||| | |
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttg-gattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6

tcgtataaatagctgcattgcgacacaattaaaattagtag-gacctgacgtgtatcctttg--cagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT-------------------------------------------------------------------------------
   |   |   |   |  || | | |        |||||   |  ||||  |  |   |  |      || |||  ||     |        |  |     |||| |||||||||   |||||||| || | ||||||| | || || |||||  | || || |||||||| ||||||||||||||||||||  | ||| | |                                                                               
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatc----aggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 6

tcgtataaatagctgcattgcgacacaattaaaattagtag-gacctgacgtgtatcctttg--cagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
   |   |   |   |  || | | |        |||||   |  ||||  |  |   |  |      || |||  ||     |        |  |     |||| |||||||||   |||||||| || | ||||||| | || || |||||  | || || |||||||| ||||||||||||||||||||  | ||| | |
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatc----agGCTCTTGGAAAGCATGGTATCATTTGCACTGAGGATTTGATCCACGAGATTCTAACAGTAGGACCTCATTTCAAGGAAGCCAACAACTTCCTTTGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00150.t01 (Vitis vinifera), 3'ss of exon 1

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
                                                                                                 |||||  | || ||||| ||||| || || || || ||||| |||||||||||| | |||||||||||||| || ||||| |||||||||||  ||||| | |
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgt-atcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
                 ||   |    |||     |  | |      | | |  ||  |||||  |   ||    || | |  |   ||  |  ||  |||||  | || ||||| ||||| || || || || ||||| |||||||||||| | |||||||||||||| || ||||| |||||||||||  ||||| | |
----------------gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttatcttg--ttgctaacctgcttttgtgatg-atagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00070.t01 (Vitis vinifera), 3'ss of exon 2

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatga-attctgttgattttgtg-tagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
                                                                          || ||  |  ||| |  | |  || |||||  | || ||||| ||||| || || || || ||||| |||||||||||| | |||||||||||||| || ||||| |||||||||||  ||||| | |
--nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 5

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgt-atcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
                 ||   |    |||     |  | |      | | |  ||  |||||  |   ||    || | |  |   ||  |  ||  |||||  | || ||||| ||||| || || || || ||||| |||||||||||| | |||||||||||||| || ||||| |||||||||||  ||||| | |
----------------gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctatatcttg--ttgctaacctgcttttgtgatg-atagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 6

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatga-attctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
             |   |||      || ||| |||  || |  | || || | | || |  | ||  ||  |   |||| ||| || |   ||  || ||||  | || ||||| || ||||| || ||||| |||||||| ||||||||  | |||||||| || ||||||||||| || ||||||||  | ||| | |
------------gtttgttgtaggttaaataacatttatatgttc-gatgtat-tgctataaactggcttttc--aatgacattttggtatgttattgcagGCTTTGGGCAAGTTTGGAATCATTTGCATTGAAGATCTCATCCATGAGATTATGACTGTTGGGCCACACTTCAAGGAGGCAAACAACTTCCTGTGGCCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
                 ||   |     |  |  || ||      ||| |   ||  |||||  |   ||    || | |  |   ||  |  ||  |||||  | || ||||| || || || || || || ||||| |||||||| ||| | |||||||||||||| || ||||| |||||||||||  ||||  | |
----------------gtttttatgtcctgtatcttggttttttttgaggg--attgtttgctatatcttg--ttgctaacctgcttttgtgatg-atagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ23123 (Selaginella moellendorffii), 3'ss of exon 5

tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttca---cctgatgaattctg--ttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
                                               |||    |  | | |  ||| |||     || ||   ||||   ||| | ||    ||   || || ||||  || ||||| ||||| ||||||||||| || ||||||| ||| ||||| || ||||||||||| || || ||||| || ||| |||
---------------------------------------------gtacgatccttttctacgatgacttctagttctcatcgtttcttatttgttctttctcagAGCCTGGGGAAGTATGGAATCATCTGTATCGAGGATCTCATCCACGAGATCTACACGGTTGGGCCACACTTCAAGGAGGCGAATAACTTCTTGTGGCCTT

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|162169492|gb|FC346056.1|FC346056

EST:     GGTTGTCAAGTCCACGTTTCGCCCTTACTGCCATTACCATTTTCGAGCAG                         GCCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGAT
genomic: GGTTGTCAAGT-CACGTGTCGCCCTTACTGACAATACCATTATCGAGCAGgtaccgtcct ... ttttgtgtagG-CACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGAT

EST: gi|162220042|gb|FC396519.1|FC396519

EST:     AGGTTGTCAAGTCACGTGTCGCCCTTACTGACAATACCATTATCGAGCAG                         GCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATC
genomic: AGGTTGTCAAGTCACGTGTCGCCCTTACTGACAATACCATTATCGAGCAGgtaccgtcct ... ttttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATC

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT

                                         ttgatttt  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