ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...tgatgtacatttgtaatgaattatttgaaaattaacttactgggtgtaattccttattttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA

Basic information

species	Glycine max
transcript	GLYMA16G07350.1
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G153541_T03 (Zea mays), 3'ss of exon 1

--tgatgtacatttg--taatgaattatttgaaaattaacttactgggtgtaattccttattttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA---------
  ||   |   ||||  || ||  |||||   | ||  | |||     ||  | |  |||| |  | | || |||   | | | |  || |   | || |    || |      ||||||||| ||||||  |||||| ||||||||||||||||||||||| |||||||| ||||| ||||||||||||||| |||| |||||         
cctgccctttgtttgattactggtttattgacatat--atttatctattg--actttttatctgctat-gtttgatgtaagcagcagtgtaacattttcc----ttcag-

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G153541_T02 (Zea mays), 3'ss of exon 1

-----tgatgtacatttgta-atgaattatttgaaaattaacttactgg-gtgtaattccttattt-tgtgttgtctgac-tcatgaacctatgaattctgtttcacagTTTAAGATA-TCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
      ||  |   |||         || |||||  | |   ||| ||   | || ||   ||||    | || ||||   |  |  |  || | |  | || | ||| |||     |  ||||||||| ||||||  |||||| ||||||||||||||||||||||| |||||||| ||||| ||||||||||||||| |         
tacttcgacttgggttttcctgccctttgtttgattactggtttattgacatatatttatctattgactttttatctgctatgtttgatgtaagcag-cagTGTAACATTTTCCTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATTGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCT---------

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G153541_T01 (Zea mays), 3'ss of exon 1

--------tgatgtacatttgta-atgaattatttgaaaattaacttactgg-gtgtaattccttattt-tgtgttgtctgactcatg-aacctatgaattctgtttcacagTTTAAGATA-TCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
         ||  |   |||         || |||||  | |   ||| ||   | || ||   ||||    | || ||||     |   |  || | |  | || | ||| |||     |  ||||||||| ||||||  |||||| ||||||||||||||||||||||| |||||||| ||||| ||||||||||||||            
gggtacttcgacttgggttttcctgccctttgtttgattactggtttattgacatatatttatctattgactttttatctgctatgtttgatgtaagcag-

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G343543_T03 (Zea mays), 3'ss of exon 1

tgatgtacatttgtaatgaattatttgaaaattaacttactgggtgtaattccttattttgtgttg--tctgactcatgaacctatgaatt-ctgtttcacagTTTAAGATA-TCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA---------
             |   | ||| |||||  | |    || |     ||  |  || |||    |||  | |   | ||     | | |    | || | ||| |||     |  |||||| || ||||||  |||||| ||||||||||||||||| ||||| |||||||| ||||| ||||||||||||||| |||| |||||         
------------tttccggattgtttgattactggtctattcc-catacatatttgtttctcattgattttatataattttgatgtaagcagcagtgtaacattttccttcagCCATGGGCAAGGAGAAGACTCACATCAACATTGTGGTCATTGGACATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTCGGCGG

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G343543_T04 (Zea mays), 3'ss of exon 1

------tgatgtacatttgtaatgaattatttgaaaattaacttactgggtgtaattccttattttgtgttg--tctgactcatgaacctatgaatt-ctgtttcacagTTTAAGATA-TCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
      |    |   ||| |   | ||| |||||  | |    || |     ||  |  || |||    |||  | |   | ||     | | |    | || | ||| |||     |  |||||| || ||||||  |||||| ||||||||||||||||| ||||| |||||||| ||||| ||||||||||||||| |         
ggtacttcgactttgttttttccggattgtttgattactggtctattcc-catacatatttgtttctcattgattttatataattttgatgtaagcagcagTGTAACATTTTCCTTCAGCCATGGGCAAGGAGAAGACTCACATCAACATTGTGGTCATTGGACATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCT---------

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G343543_T05 (Zea mays), 3'ss of exon 1

---------tgatgtacatttgtaatgaattatttgaaaattaacttactgggtgtaattccttattttgtgttg--tctgactcatgaacctatgaatt-ctgtttcacagTTTAAGATA-TCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
         |    |   ||| |   | ||| |||||  | |    || |     ||  |  || |||    |||  | |   | ||     | | |    | || | ||| |||     |  |||||| || ||||||  |||||| ||||||||||||||||| ||||| |||||||| ||||| ||||||||||||||            
gggggtacttcgactttgttttttccggattgtttgattactggtctattcc-catacatatttgtttctcattgattttatataattttgatgtaagcagCAGTGTAACATTTTCCTTCAGCCATGGGCAAGGAGAAGACTCACATCAACATTGTGGTCATTGGACATGTCGACTCTGGCAAGTCGACCACCACTGGCCA------------

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110509_T02 (Zea mays), 3'ss of exon 1

-tgatgtacatt-tgtaatgaattatttgaaaattaacttactgggtgtaattccttatt-ttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA---------
 | | |   ||| | |  | | |     |         ||  |   |    || || ||| |||  | ||||| || |  |   || |  |||   ||||           | ||||||||| ||||||   ||||| |||||||||||||||||||| || |||||||| ||||| |||||||| |||||| |||| |||||         
ctaaagctgattgttttgttagtggggggggggggggtttgtttactagtgtttctaattattgattcgtctgtcttaacagtttaagc-ttcaccttca-----------aCCATGGGTAAGGAGAAGTCCCACATCAACATTGTGGTCATTGGCCACGTCGACTCTGGCAAGTCGACCACCACCGGCCACCTGATCTACAAGCTTGGAGG

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G154218_T01 (Zea mays), 3'ss of exon 1

--------------tgatgtacatttgtaatgaattatttgaaaattaacttactgggtgtaattccttat-tttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
              |  ||  |   | | || |||| | |    | |    || |     || || ||  | ||| |  |   ||| || |     ||  | |||  | ||||  |  ||     ||||||||||||||||   ||||| ||||||||||| |||||||| ||||||||||| ||||| |||||||| || ||| ||        
acgttagatctagtttctgatcccatctgataaattgtgtcgttactgg--tagtattaatatttactagtgtttctaatcgttgattcgtcttgttaacagTTCAATCTCACC-TCCAA----CCATGGGTAAAGAGAAGTCCCACATCAACATTGTGGTTATTGGCCACGTTGACTCTGGCAAGTCGACCACCACAGGACACCTG--------

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G001327_T01 (Zea mays), 3'ss of exon 1

------------tgatgtacatttgtaatgaattatttgaaaattaacttactgggtgtaattccttat-tttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
            |  | |    |   |    || | |||     | |||    |  |  | || ||  | ||| |  |   ||| || |     ||  | |||  | ||||  |  ||     ||||||||||||||||   ||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||| || ||| |         
caacgttagatctagtttctgatcccatccgataaattgtgtcgttactggtagtattaatttactagtgtttctaatcattgattcgtcttgttaacagTTCAATCTCACC-TCCAA----CCATGGGTAAAGAGAAGTCCCACATCAACATTGTGGTTATTGGCCATGTCGACTCTGGCAAGTCGACCACCACAGGACACCTT--------

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G149768_T01 (Zea mays), 3'ss of exon 1

------------tgatgtacatttgtaatgaattatttgaaaattaacttactgggtgtaattccttat-tttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
            |  | |    |   |    || | |||     | |||    |  |  | || ||  | ||| |  |   ||| || |     ||  | |||  | ||||  |  ||     ||||||||||||||||   ||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||| || ||| |         
caacgttagatctagtttctgatcccatctgataaattgtgtcgttactggtagtattaatttactagtgtttctaatcgttgattcgtcttgttaacagTTCAATCTCACC-TCCAA----CCATGGGTAAAGAGAAGTCCCACATCAACATTGTGGTTATTGGCCATGTCGACTCTGGCAAGTCGACCACCACAGGACACCTT--------

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110509_T03 (Zea mays), 3'ss of exon 1

-------tgatgtacatt-tgtaatgaattatttgaaaattaacttactg---ggtgtaattccttat-tttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
       |||||    || |  |    ||| |||    | |        |   ||| |  || ||  | ||| |  |   ||| || |    ||    | | |      ||  || |   | ||||||||| ||||||   ||||| |||||||||||||||||||| || |||||||| ||||| |||||||| |||||| |         
atgtgtatgatgctttttctaaagctgattgttttgttagtggggggggggggggtttgtttactagtgtttctaattattgattcgtctgtcttaacagTTTAAGCTTCACCTTCA---ACCATGGGTAAGGAGAAGTCCCACATCAACATTGTGGTCATTGGCCACGTCGACTCTGGCAAGTCGACCACCACCGGCCACCT---------

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G151193_T01 (Zea mays), 3'ss of exon 1

tgatgtacatttgtaatgaattatttga-aaattaacttactgggtgtaattccttatt--ttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA---------
       || || | |       | | | |||||   ||| |||| ||  ||   || |  || |  |   ||| || |    ||    | | |      |   |  ||    ||||||||| ||||||  |||||| ||||||||||| |||||||| || |||||||| ||||| || ||||| |||||| |||| |||||         
-------cagttttgacc--ccgtctaataaattttgttagtgggagttgtttactagtgtttctaattattgattcgtatggcttaacagtttaagcttcgcctccag-

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G096662_T01 (Zea mays), 3'ss of exon 1

tgatgtacatttgtaatgaattatttgaaaattaacttactgggtgtaattccttattttgtgttgtctgactcatg--aacctatgaattctgtttcacagTTTAAG----ATATC-----ATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
       | ||| |||    | ||   |   |||  ||| ||| | || |    | |  ||| |  |    ||  |   ||   ||  ||   |||| | ||||||||    || ||     ||||| || |||||    ||||| ||||||||||| ||||||||||| |||||||| ||||| || |||||||||||| |||| ||   
------gcttttttaa--gctgatggaattgttatgttagtggctttagtattgtgtgatgtttactagtgcttctaataattgattcatctggtttgatagtttaagCTTCATCTCCAGCGATGGGCAAGGAGAAATCCCACATCAACATTGTGGTTATTGGCCATGTCGACTCTGGCAAGTCGACTACCACTGGCCACCTGATCTA---

upper sequence: GLYMA16G07350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G151193_T02 (Zea mays), 3'ss of exon 1

-----------tgatgtacatttgtaatgaattatttga-aaattaacttactgggtgtaattccttatt--ttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA
           | |  | || || | |       | | | |||||   ||| |||| ||  ||   || |  || |  |   ||| || |    ||    | | |      |   |  ||    ||||||||| ||||||  |||||| ||||||||||| |||||||| || |||||||| ||||| || ||||| |||||| |         
cggtttcaacgttagattcagttttgacc--ccgtctaataaattttgttagtgggagttgtttactagtgtttctaattattgattcgtatggcttaacagTTTAAGCTTCGCCTCCAG---CCATGGGTAAGGAGAAGTCTCACATCAACATTGTGGTTATTGGCCACGTCGACTCTGGCAAGTCGACAACCACCGGCCACCT---------

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|209712611|gb|BW653744.1|BW653744

EST:     AGTCTCTGAATTGCGGCTGAGGGTTTCGAGTAACGNNNNNNNNNC-TGAG                         TTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTG
genomic: AGTCTCTGAATTGGGGCTGAGGGTTTCGAGTAACGTTTATTTTTCACGAGgtataatctt ... tgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTG

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtaattccttattttgtgttgtctgactcatgaacctatgaattctgtttcacagTTTAAGATATCATGGGTAAAGAGAAGGTTCACATTAACATTGTGGTCATTGGCCATGTTGACTCTGGGAAGTCAACCACCACTGGCCACTTGATTTACAA

                    gtctgac  putative branch site (score: 3)
                                          ttctgtttc  putative PPT
        ttattttgt  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