ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA

Basic information

species	Physcomitrella patens
transcript	PP1S169_48V6.2
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8

gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
                                                  |  |||  | |   |||| |  | | |    || ||  ||  |||||   ||  || ||  |     | |||||   |  ||  ||  || ||      | || |||| |  |  | ||||| || |||||| | || ||||| || || ||||||||||| ||||||||||||||||||||||| |||| |||  || | ||||  |
--------------------------------------------------gtgtgcc-tctgctttgatgcagtatcaaa-atttgcatat-agttt---cattttatagttt----gattttatctactttgttt--gtttga-----tattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 9

gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
                                               ||||  ||  ||||   |        || |   | | ||     |  | ||   || |     ||    |  ||||     | | ||  |   ||    | | | || |||||  |  |  ||||||| |||||| | |||||||| |  || || |||||||| ||||||||||||||||| || || || |  ||| | || || | ||
--------------------------------------------ttggcagtctgtaatttcttt--------aatctcac-tttgcaccagcatcttccaaagtacatgatattgatattttt----tttgaccctttcatata-tatatatttcagCTGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 9

gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacg-aggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggt-cttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
                                                           |||  ||   | || |  |    ||||| ||      || | |   ||| |||   ||| | |    | || |   | || |||    | |   ||| ||||| ||  || |||||||||||||  | || ||||| || || || |||||||| ||||||||||||||||| || || || | |||| |  | || | ||
----------------------------------------------------------cttatttttgtgtagcatgcactgatctgagttttctgttatcct-tttgcaaaca-acatgataccaagatttgtttctaatattttcttccaattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9

gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
                                                                      ||       | || |  |||    ||| || |   ||| ||  ||   ||  | || ||  | ||   |||| |    | | |||||| | |  ||  ||||||| |||||| | || |||||||| || ||||| ||||||||||| || ||||||||||| || |||| |||  ||||||| | ||
-------------------------------------------------------------------gtaagttgtaaagaattttagtaatgttttatggatgctgtcaa--catttgtcgttgacatgatgctgatgtat-ctacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9

gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcat-ctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtat-gcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
                               | | || |      |  || ||||||    ||     |   ||  |  |  | || | ||    |  |    |     |||   | | |     | |   | | ||| | || |   | | | || ||||| ||||| || ||||  |||||| | |||||||||||||| ||||| |||||||| ||||| |||||||| || || || | |||  || | || | ||
------------------------------gtaagatatc-----ccacaacttgctgggaaatccttccctgacccctgtttgctctttatttatactcttgagccccaaa---ataagcacatggaccttaattttggaattgttatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 8

------gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaa-acgggcatctgtg-----taggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
       ||   || ||  |||| ||      ||| |   ||| |     | | | | |||  || ||    ||| |  |  |      ||||||     || |  || ||   |        ||  |    ||||   ||  |  ||    || | ||   |  | ||| | ||||| || ||||| |||||| | || ||||||||||| ||||| ||||| || ||||| ||||||||||| || || | |||  || |||| |  |
gtaagatttctttctacccttcaagca---cctttataagaatctcatcaagttctgtttgaaatatacaaggactatcatcatccaattctgtgctttataaggattattatcatccacttctgtgc----tttactgatagtgtttataaattctgttcatcatccagTTGTTCTATTTAAGTGGCATTCTCACTGTATTCTTTTGCGGGATTGTCATGTCACACTACACCTGGCATAACGTGACTGAAAGTTCAAGAGTCACCACAA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 8

gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttact-ttagta-tgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
                  |  |  | | | || |  | || |  ||| |  || ||   |    |  |   | |    |   ||| | |||    ||   ||     || ||  |    ||  ||   |   | | ||||||     |  | |  ||||||| ||||| |||||||| |||||| | || || || || || ||||||||||| |||||||| ||||| || || || |||| |||  || |||| | ||
------------------gtaagatttcttttaacttcttgggcacttcc-ctggcccctgttgtctattggcattgagtgttctatttaga---ttcaacagtagatatatcaatcatttaaagtctttccattgttagtaactttggttgtcctgcagCTATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 7

gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
                                                                                       ||   |||||||      | || |     ||  |||     ||||  | |   |||||       || ||||| |||||| ||||||| || ||| |||| |||||||| |||||||| ||||| ||||| || ||||| |||||||||||||  ||  ||||||||| ||
---------------------------------------------------------------------------------------gtgatagttttt-ttctgtatagagaggtagcatttct---tcttgttct--catgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 7

gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA
                                                                                       ||  ||||||||      | || |     ||  |||     ||||  | |   |||||       || ||||| |||||| ||||||| || ||| |||| |||||||| |||||||| ||||| ||||| || ||||| |||||||||||||  ||  ||||||||| ||
---------------------------------------------------------------------------------------gtgagagttttt-ttctgtatagagaggtagcatttct---tcttgttct--catgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA

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|162255349|gb|FC432075.1|FC432075

EST:     AAATAGCAATCATGACATTGATGGCGTATTTATCTTACGTCTTTGCAGAG                         CTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATG
genomic: AAATAGCAATCATGACATTGATGGCGTATTTATCTTACGTCTTTGCAGAGgttagctcga ... ttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATG

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA

                        atcttac  putative branch site (score: 3)
                                           tcttttttgc  putative PPT
                ttttagaaatctta  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