ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtcaacggtgacagccttactgtactttttgcatattgaaatacttggagatcctcttatgaccaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG

Basic information

species	Physcomitrella patens
transcript	PP1S31_251V6.1
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g39440.1 (Oryza sativa), 3'ss of exon 3

gtcaacggtgacagccttactgtactttttgcatattgaaatacttggagatcctcttatgaccaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
                             ||   ||||    | || |  ||  | |||||        ||      ||| || |  ||| |   ||||   |  || || |||   | ||| || || ||||||||| ||||||||||||||||||||||||  ||  ||||  | || || || |     || || 
----------------------------gtgtgaattgt--caatttgtcatgttattatgttactgtgatgacaatatt-gt-cttgataatgccagGCAATTTGGGCCTGTCTCCGGTGTGCGAATTCCCTATCAGGAGAAGCGGATGTTTGGTTTTGTGAGCTTCCTATACACTGAGACAGTGAGGCTTATCTTA

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3

gtcaacggtgac--agccttactgtactttttgcatattgaaatacttgga-gatcctcttatgaccaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
|| |    ||     |  | ||| |  |   ||    |     | | | |  | ||       ||   || || ||     |||        |   || ||    || |||||||||||||| ||  ||||||| || ||||||||||| |||||||||||||| || ||||| ||| |||| || || ||    ||| | 
gttattattgtttaggtttaactttgttaactggg-gtcagtgtgcatagttggtcaatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA12G01350.1 (Glycine max), 3'ss of exon 2

gtcaacggtgac--agccttactgtactttttgcatattgaaatacttgga-gatcctcttatgaccaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
|| |    ||     |  | ||| |  |   ||    |     | | | |  | ||       ||   || || ||     |||        |   || ||    || ||||| |||||||| ||  ||||||| || ||||||||||| |||||||||||||| || ||||| ||| |||| || || ||    ||| | 
gttattattgtttaggtttaactttgttaactggg-gtcagtgtgcatagttggtcgatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCTGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3

gtcaacggtgac--agccttactgtactttttgcat--attgaaatacttggagatcctc---ttatgaccaatcaattttctca---tttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
|| |    ||     |  |  |||||  ||| || |  | ||  ||  |||   ||  |        | |  |   |||  ||     |||        |   || ||   ||| || ||||| ||||| ||  ||||||| || ||||||||||| |||||||| ||||| || ||||| ||| |||| ||||| ||    ||| | 
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G21100.1 (Arabidopsis thaliana), 3'ss of exon 1

---------gtcaacggtgaca--gccttactgtactt-tttgcat-attgaaatact--tggagatcctcttatgaccaatcaattttctcatt--------------tgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
           |||  ||  ||  ||  |  |||  || ||||||| ||| |||   |  ||||  ||  || |||          | | | |||              | ||  |  |   || ||   ||  || ||||| ||||||||| |||| || || |||||||| ||||||||||| ||||| |||||| |  | || |||||||| | |   || |||
gtaatcttttacaattgtatcaaagctgttatgtgtttgtttgcatcattaaaagtttggtggatgtctactaatgtttgcctggctctgttattgtagactgattatgtttgttgttttcttgtagCAATTTTGGACCAGTGCAAGATGTTAGGATTCCATACCAGCAGAAACGGATGTTTGGGTTTGTCACTTTTCTCCACTCTGAAACTGTGAGAATCATATTG

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G12440.3 (Arabidopsis thaliana), 3'ss of exon 3

---------------------------------------------------------------------------gtcaacggtga--cagccttactgtactttttgcatattgaaatacttggagatcct-cttatgaccaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
                                                                              |  | | |  |||   | || |  ||  |  || |   |  | |    |||    | | |||  ||  ||  ||   |||  |  |   |  ||| ||    |  ||  ||||||||||||| |||||||| || || |||||||| |||||||| |||||  | ||||   || | || || || ||||   |  | 
gtattactggacaaccatctctgtctaacaagtgctcgttcttgtatatttatatggaagaattggcaaataagtagtattgattaatcagttgttctttggttaattgatgtctgacaattcatggatgtggcgtttgagaaaataacatt---attgatttgttgtctatgaagCCTCTTTGGAACAGTCCAAGATGTGCGGATCCCATACCAACAGAAGCGTATGTTTGGCTTTGTTTCATTTGCTCATCCCGAGACAGTGAAAGTTGTACTA

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G51950.1 (Arabidopsis thaliana), 3'ss of exon 4

gtcaacggtgacagc-cttactgtactttttgcatattgaaatacttggagatcctcttatg-accaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
|| |      |||   |  | || ||||||      |   |||   ||    | ||  ||||   ||    || || | ||        | ||  |  ||  |||  || ||||| ||||||||  |||| || |||||||| ||| | ||||||||||||||||| ||||| ||  | || ||||||||    ||| | 
gtaatttccaacaaaacacattgaacttttatttggtctgaatgtatg----ttcttgtatgtgacataagatgttgttat--------ggtggttatagTACTTTTGGACCAGTTCAAGATGTGAGGATACCATATCAGCAAAAGAGAATGTTTGGTTTTGTGACATTTGTGTACCCTGAGACTGTTAAGAGCATTCTC

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3

--------gtcaacggtgacagccttactgtactttttgcatattgaaatacttggagatcc---tcttatgaccaat---caattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
          |||   | |     |   | |   |||||   | |  |||  | |||  |      |||  |     |    || |  ||  |||||   |  |   || ||   || ||||||||| ||||||||  ||||||| |||||||||||| ||||||| || ||||| || || || ||| |||| || || ||    ||||||
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctgttttgttttg--ttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ06262 (Selaginella moellendorffii), 3'ss of exon 5

gtcaacggtgacagccttactgtactttttgcatattgaaatacttggagatcctcttatgaccaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
                                    |  |  | ||  ||    | |  |           | ||| |     |  |  |   || ||  |||| ||||||||||| |||||||| || || || ||||||||||| |||||||| || || || ||  | ||| | || ||||| || || ||  ||
-----------------------------------gtagatcaattctagtgtttttctttcttttcttgctctctaa---acgaagtttttgtgtagATCTTATGGTCCAGTCCAGGATGTTCGAATTCCATACCAGCAGAAGCGAATGTTTGGATTCGTCACCTTCATCTATCCCGAGACTGTCAAGGCGATACTG

upper sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ18963 (Selaginella moellendorffii), 3'ss of exon 3

gtcaacggtgacagccttactgtactttttgcatattgaaatacttggagatcctcttatgaccaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG
                                    |  |  | ||  || |  | |  |   |  |   |  |||||     |  |  |   || ||  |||| ||||||||||| |||||||| || || || ||||||||||| |||||||| || || || ||  | ||| | || ||||| || || ||  ||
-----------------------------------gtagatcaattctagtttttttctt--tcttttcttgctctcaaa-acgaagtttttgtgtagATCTTATGGTCCAGTCCAGGATGTTCGAATTCCATACCAGCAGAAGCGAATGTTTGGATTCGTCACCTTCATCTATCCCGAGACTGTCAAGGCGATACTG

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|162209786|gb|FC385720.1|FC385720

EST:     TTTCCTGCCGAATCTACTTTTTGTGAAGAGGATGTAACATCACATTTCAG                         GGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGAT
genomic: TTTCCTGCCGAATCTACTTTTTGTGAAGAGGATGTAACATCACATTTCAGgtcaacggtg ... atgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGAT

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cttggagatcctcttatgaccaatcaattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG

                     aatcaatttt  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