ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...gttgattgttagttatctgctattttacactatcttgtgcttatcctattaccttattacataatctaacctgttgtcgtggttgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA

Basic information

species	Glycine max
transcript	GLYMA09G34760.3
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1

gttgattgttagttatctgctattttacactatcttgtgcttatcctattaccttattacataat-ctaacctgttgtcgtggttgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA------
  | ||     ||    |  |  |  | ||| |          |  ||  |    ||  ||| || || |    ||||  | |||   |||  |||   |||||||  ||  ||||||| ||||| ||||| || ||||| || || ||||||   |||||||||||||||||||| ||||| |||||||| ||||| ||       
--taatctggtgtggatttttgctgca-actgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgt---aggtaagGTAAG-CCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g37970.1 (Oryza sativa), 3'ss of exon 1

-----gttgattgttagt-tatctgctatt-ttacactatcttgtgcttatcctattacct--tattacataatctaacctgttgtcgtggttgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA
      | |||||   ||  || || | |     |  ||| | | | |  |  || |  ||  | | |  |       | ||||   ||| |   |     |  | | |  | |   | |  ||||| ||||| ||||| |||||||| || || ||||||   |||||||||||||||||||| ||||| ||||||||          
atgtgctcgattgcgcgtgcatatggtctcgccgctgtatatcgggttgttggtagtcgctgatgtgaggtttgtgttcgtgtttgtgtgatgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAATGGCCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAAC---------

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g02510.3 (Oryza sativa), 3'ss of exon 1

gttgattgttagttatctgctatt-ttacactatcttgtgcttatc-ctattaccttattacataat-ctaacctgttgtcgtggttgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA-
 |   |  |  | | |    | ||  | ||     | ||         ||  |    ||  ||| || || |    ||||  | |||   |||  |||   |||||||  ||  ||||||| ||||| ||||| || ||||| || || ||||||   |||||||||||||||||||| ||||| |||||||| ||||| ||  
ttcagtaatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgt---agGTAAGGTAAG-CCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCC

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G409407_T01 (Zea mays), 3'ss of exon 1

gttgattg-ttagttatctgctattttacactatcttgtgctta-tcctattaccttattacataatctaacctgttgtcgtggttg--actttaatgtgta-------agGTAAGCCAAAACC----ATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA
  ||  || || | |||| |   |  |   ||| |  |     |    |     ||   |   |  |  | |  | || |||||||    | || | ||| |       |||||||  | |       ||||| ||||| ||||| |||||||| ||||| ||||||   |||||||||||||||||||| ||||| ||||||            
--tgcctgctttgatatc-gtgctgctgggctaacgaggatggagctttggcggctccgtttgttgttcagctggatgacgtggttattgcattgacgtgcagGTAAGAAGGTAAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTTATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTC------------

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G081102_T03 (Zea mays), 3'ss of exon 1

----gttgattgttagttatctgctattttacactatcttgtgcttatc-ctattaccttattacataat--ctaacctgttgtcgtggttgactt-taatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA
    | ||   |    |  |    | || | | |  |  ||||||  |  ||  |  ||  | |     |  ||     ||||| |  ||  ||   |||   | |  | |||        ||||| ||||| ||||| || ||||| ||||| ||||||   |||||||||||||||||||| ||||| |||||||| ||       
tggagctggcggcagctcgttgattcttgttc-ccgtggtgtgctcgttgctcgtctctgctgatgccgtcactgttgcgttgttgatgtgtacaggtaagAAGGAGAGAAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCA-------

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G145280_T01 (Zea mays), 3'ss of exon 1

--gttga-ttgttagttatctgctattttacactatcttg-tgcttatcctattaccttatt-acataatctaacctgttgt--cgtggttgactttaatgt--gtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA
   | ||  |||| |      | |  ||     |  | || || || |  |    |     | ||    |      || |||  ||| |||||  |  | ||  | |  | |||        ||||| ||||| ||||| || ||||| ||||| ||||||   |||||||||||||||||||| ||||| ||||||||          
agatggagctgttggcagctcgttgattcttgttcccgtggtgtttgttgttcgtctcggctgacgccgttgctgttgatgtggcgttgttgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAAC---------

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G081102_T01 (Zea mays), 3'ss of exon 1

---------gttgattgttagttatctgctattttacactatcttgtgcttatc-ctattaccttattacataatc--taacctgttgtcgtggttgactt-taatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA
         | ||   |    |  |    | || | | |  |  ||||||  |  ||  |  ||  | |     ||  |     ||||| |  ||  ||   |||   | |  | |||        ||||| ||||| ||||| || ||||| ||||| ||||||   |||||||||||||||||||| ||||| ||||||            
tagggtggagctggcggcagctcgttgattcttgttc-ccgtggtgtgctcgttgctcgtctctgctgatgccgtcactgttgcgttgttgatgtgtacagGTAAGAAGGAGAGAAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTC------------

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: AT3G49010.1 (Arabidopsis thaliana), 3'ss of exon 1

gttgattgttagttatctgctattttacactatcttgtgcttatcctatt----accttattacataatctaacctgttgtcgtggttgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA--
 ||   | || |   | ||   |||||   | |  | | |||   || ||       | || |  | || |||  ||| ||| || ||||  ||  |  | |   | ||   ||   |||   ||||| |||||||||||||| || || ||||||   |||||||||||||| ||||| ||||| |||||||| ||||| ||   
-ttttgtttttgaagtttgaggttttatcatttgatttccttgagctgtttaaagtttcatcatttgatttaaagtgt-gtc-tgattgatgttttttggcagCTTGAGTTGAAGAAATG---AAGCACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAG

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 1

gttgattgttagttatctgctattttacactatcttgtgcttatcctattaccttattacataatctaacctgttgtcgtggt-tgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA------------
    | ||||  || | |   ||     | ||   |     | |   ||||  ||| | |    | ||   | || || || | | || ||  ||| |   ||     | ||  |||   ||||| ||||| |||||||| | |  |||||| || |||||||||||||| ||||| ||||||||||| || ||||| ||             
---taatgttgcttgtgtaacatg----attagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgtaacatttgtgttt---gttgcttagAAAAATG---AAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S21_106V6.1 (Physcomitrella patens), 3'ss of exon 1

--gttgattgttagttatctgctattttacactatcttgtgcttatcctattaccttattacataatctaacctgttgtcgtggttgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA---
    |     ||  |  |    || ||| ||   |    ||  |      |||  |   |    ||   ||| |   ||    | ||   ||  |  | | |   |||    |||||||| ||||||||||| || || || || || ||||||   ||| |||||||||||||||||| |||||||||||| ||||| |||   
gccctccgccttgatgcttcagtagtttgcatggtgcattgtatcagggtttaggtctgtgggaaaaaaaacgtagggtttctgatggtgttgct-cgcagGTCTAGC----ACCATGGTGAAGCATAACAACGTCATTCCCAATGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACTTGGTTCAACCAGCCCGCACGC

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S47_277V6.1 (Physcomitrella patens), 3'ss of exon 1

----------------------------------------------------------------------------------------gttgattgttagttatctgctattttacactatcttgtgcttatcctattaccttattacataatctaacctgttgtcgtg-gttgactttaatgtgtaagGTA-----AGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA---
                                                                                        |  ||| ||  ||     | | ||   |   | |  | |   |||   ||  | |      |   |     |||||  ||    | | |||   ||       |      | | |||||||||| |||||||||||||| ||||| |||||||| |||   ||| ||||||| |||||||||| ||| |||||||| ||||| ||    
gtgtgcctcgccgctcatcttaacattgtacagcttcataggcttccagttgggaaggagtttgtggttgcttgtgcaattccttgtgggagatggtctgtccaaagttcttccccctaaacgggaggcgatctagttctcctgaggggtgtgcatggttgttgatgtatactaagtttttggtcatcaccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAAGAAGGACTGGCAAAACTATGTGAGGACGTGGTTCAACCAGCCCGCTCGC

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S459_9V6.2 (Physcomitrella patens), 3'ss of exon 1

------------------------------------------------------------gttgattgttagttatctgctattttacactatcttgtgcttatcctattacctta-------------ttacataatctaacctgttgtcgtggttgactttaatgtgtaagGTAAG-CCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA---
                                                            | ||   |     | |||   |    |    | || | ||| | | |   | || |             ||   || | |  | ||    |     ||  | |  ||   || ||| | ||| || |||||| |||||||||||||| ||||| ||||| ||||||   ||| |||||||||||||||||| ||| |||||||| ||||| |||   
gtatgctggcttgctttcctttgcattgcacagctgcgtaaggttgtggctggggatcgtgctgtaagactcatttctttcaggagaattcagctggagctcagcttcggagctgaaggcgacttaggtttgtttagtttttcatgcccactaaactgcttgtcgtgaaaaacgtagGACCAGAATCATGGTGAAGCATAACAATGTCATCCCCAACGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCACGC

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S459_9V6.1 (Physcomitrella patens), 3'ss of exon 1

------------------------------------------------------------gttgattgttagttatctgctattttacactatcttgtgcttatcctattacctta-------------ttacataatctaacctgttgtcgtggttgactttaatgtgtaagGTAAG-CCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA---------
                                                            | ||   |     | |||   |    |    | || | ||| | | |   | || |             ||   || | |  | ||    |     ||  | |  ||   || ||| | ||| || |||||| |||||||||||||| ||||| ||||| ||||||   ||| |||||||||||||||||| ||| |||||||| ||||| |||         
gtatgctggcttgctttcctttgcattgcacagctgcgtaaggttgtggctggggatcgtgctgtaagactcatttctttcaggagaattcagctggagctcagcttcggagctgaaggcgacttaggtttgtttagtttttcatgcccactaaactgcttgtcgtgaaaaacgtaggaccagAATCATGGTGAAGCATAACAATGTCATCCCCAACGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCACGCAAGAAG

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S58_38V6.1 (Physcomitrella patens), 3'ss of exon 1

gttgattgttagttatctgct-attttacact-atcttgtgcttatcctattacctt----attacataatctaacctgttgtcgtggttgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA---
 |||      |||    |||  || ||   ||  ||| |   |  || |||    ||      |  || |  ||||  | |||||  || |   |  || |  | |||  ||    |||||||| |||||||| ||||||||||| || || ||||||   ||| |||||||||||||||||| ||| |||||||| ||||| ||    
-ttgtgatggagtggcgtgccgatgttgttcttgtctcgcattcctcatatagggtttaagggtttatgacataac--gatgtcggagtcggtct--attttcagGGTTGGC----ACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCCCGC

upper sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S126_52V6.1 (Physcomitrella patens), 3'ss of exon 1

gttgattgttagttatctgctattttacactatcttgtgcttatcctattaccttattacataatctaacctgttgtcgtggttgacttta--atgtgtaagGTAAGC-CAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA----
      ||| |   |   ||   |||      | ||||  | || |  | |    || |            |||||  || |     |||   ||||||| |  |||     || |||||| |||||||||||||||||||| || || ||||||   ||| ||||||| |||||||||| ||| ||||| || ||||| ||     
------tgtgatggagtggcgtatttttgtgttgttgttgtaattc-gtgaagcaataattagggtcggattgttgatgtcgcaatttttgtgatgtgtatgtgaagAGTTGAAACATGGTGAAGCATAACAATGTTATCCCCAATGGCCACTTCAAGAAGGACTGGCAAAACTATGTGAGGACCTGGTTTAACCAGCCCGCCCGCA

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|10844041|gb|BF067378.1|BF067378

EST:     GTTTTGTTCATTGTTTTTCTGGATTCGTAGTGCTTGGGATTTAATTAGAG                         GTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTT
genomic: GTTTTGTTCATTGTTTTTCTGGATTCGTAGTGCTTGGGATTTAATTAGAGgtagagctat ... aatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTT

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctattaccttattacataatctaacctgttgtcgtggttgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA

        ttattacataatctaa  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