ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG

Basic information

species	Oryza sativa
transcript	LOC_Os01g60700.1
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G380227_T01 (Zea mays), 3'ss of exon 2

--gttactgcttctaaactttttctttt-tgacattac-caataagtgaatattta---ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG-
  |    |||| ||  | || |  | || || ||| || ||| | |||    ||||   |||||  | |   |  |  ||| |   | ||  |    || ||  ||  |||| ||  |||| |||| |  |||| |||| |||||||||||||| || |||||||| |  ||||||||||| || |||| ||||||||| ||||| ||||||||||| |||||||| |||||||||||||||  
gtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacaatatcttataatacc-gagctgctgacttaa-ctggtatttatatttccatttgtttttcagGCCATGTACAACGAGTTCTCAAC-TTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGAT

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G143790_T01 (Zea mays), 3'ss of exon 1

--gttactgcttctaaactttttctttt-tgacattac-caataagtgaatattta---ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG
  |    |||| ||  | || |  | || || ||| || ||| | |||    ||||   |||||  | |   |  |  |||||   | ||  |      ||  |  |  | ||||  |||| |||| |  |||| |||| |||||||||||||| || |||||||| |  ||||||||||| || |||| ||||||||| ||||| ||||||||||| |||||||| ||||||||||||||| 
gtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacattatcttataataccgagcc--gctgacttaacttgtatttatatttccatttgtttttcagGCCATGTACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G380227_T02 (Zea mays), 3'ss of exon 2

-------------------------------------gttactgcttctaaactttttctttt-tgacattac-caataagtgaatattta---ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG-
                                     |    |||| ||  | || |  | || || ||| || ||| | |||    ||||   |||||  | |   |  |  ||| |   | ||  |    || ||  ||  |||| ||  |||| |||| |  |||| |||| |||||||||||||| || |||||||| |  ||||||||||| || |||| ||||||||| ||||| ||||||||||| |||||||| |||||||||||||||  
gtctagctttcttgcatgatgaaggaccctttcaggtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacaatatcttataatacc-gagctgctgacttaa-ctggtatttatatttccatttgtttttcagGCCATGTACAACGAGTTCTCAAC-TTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGAT

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G079117_T01 (Zea mays), 3'ss of exon 1

--gttactgcttctaaactttttctttt-tgacattac-caataagtgaatattta-----ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG
  |    |||| ||  | || |  | || || ||| || ||| | |||    ||||     |||||  | |   |  |  |||||   | ||  |      ||  |  |  | ||||  |||| |||| |  ||||  ||| |||||||| ||||| || |||||||| |  ||||||||||| || |||| ||||||||| ||||| ||||||||||| |||||||| ||||||||||||||| 
gtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttttatttggcattcaaccacattatcttataataccgagcc--gctgacttaacttgtatttatatttccatttggttttcagGCCATATACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G068151_T01 (Zea mays), 3'ss of exon 3

gttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggttta---aactcttattcatatgtt-attttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG
                          |||   | | | |   |  ||  |  | |   ||| |   ||   |||   | ||    |||   |||  |  | | |   ||||  |||| |||| |  |||| |||| |||||||||||||  || |||||||| |  ||||||||||| || |||| ||||||||| ||||| ||||||||||| |||||||| ||||||||||||||| 
-------------------------gtgatcatgctacttgatttatggtcttatgggcta-tggcatcacacaaaaggtgtgcttttaataccgagccgctgacttaacttgtatttatatttccatttgtttttcagGCCATGTACAGCGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G010453_T01 (Zea mays), 3'ss of exon 1

--gttactgcttctaaactttttctttt-tgacattac-caataagtgaatattta---ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG
  |    |||| ||  | || |  | || || ||| ||  || | |||    ||||   |||||  | |   |  |  |||||   | ||  |    || |   ||  |||| ||  |||| |||| |  |||| |||| ||||| | |||||| || |||||||| |  ||||||||||| || |||| ||||||||| ||||| ||||||||||| |||||||| ||||||||||||||| 
gtgagcatgctacttgatttatggtcttatggcatcacataaaaggtgtgcttttaattttttatttggcattcaaccacattatcttataatacc-gagccactgacttaa-cttgtatttatatttccatttgtttttcagGCTACGTACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G828466_T01 (Zea mays), 3'ss of exon 1

--gttactgcttctaaactttttctttt-tgacattac-caataagtgaatattta---ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG
  |    |||| ||  | || |  | || || ||| ||  || | |||    ||||   |||||  | |   |  |  |||||   | ||  |    || |   ||  |||| ||  |||| |||| |  |||| |||| ||||||| |||||| || |||||||| |  ||||||||||| || |||| ||||||||| ||||| ||||||||||| |||||||| ||||||||||||||| 
gtgagcatgctacttgatttatggtcttatggcatcacataaaaggtgtgcttttaattttttatttggcattcaaccacattatcttataatacc-gagccactgacttaa-cttgtatttatatttccatttgtttttcagGCCACGTACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3

gttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG
                  ||| |||||   | ||      |||||||    |||| |    |||||  | ||  | |||| |       ||   |  | | | | |  ||||||          ||| | | ||||| ||||| ||||| ||||||||  | ||||| || |||||||||||||||| ||||||||| ||||||||||| |||||||||   | | ||||||| |
-----------------atttgtttttcgtagtatg---gagtgaatg---atttcaagatgttatg-attat-taggttaactacacatgttatctttgctgacatccttatt----------tttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 2

gttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG-
  |||  ||   | |    ||  |||||   ||   | || |     | | |||| |  || |  |||  |   | |||| ||   | |  || || |  ||    ||   || | | |    || |  ||  |||| ||||| ||||| ||||||||  | ||||| || ||||||||||||||||  |||||||| ||||||||||| |||||||||   | | |||| || | 
--tacaactataataacactttgttttgtttttcatagtatggagcgaatgatttcaagta-tgttatgattattaggttaat---tatacactttatcttt---gctgacatccttct----ttctgcttgtaggCTATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGCGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAAGAAGA

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0058g01290.t01 (Vitis vinifera), 3'ss of exon 3

gttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG
                    | |   | | || ||         | | | ||| |||   | || | |  | || |||||| || || |||   |||||   | |   |||     | ||||        ||||||| ||||||||||| || |||||  | || || || |||||||| ||||| | ||||||||| || |||||||| || |||||   || | | || |  |
--------------------tttccctcagatcactgtc--ccaattctgtatattagg-attttttttttccagtggttgttg-ttcttg---ttgtgtactgagaacttccctgtgtgtt--------tacagGCTATGTACAATGAATTTTCAACTGCCAATATACAGATTGACAAGGATTTTAGTGCAAAGCTTTCGGGATATGGTTGCGTTGGCCACATTCCAGAAGCAG

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|29684563|gb|CB680838.1|CB680838

EST:     TTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAG                         GCCATGTACAATGACTT
genomic: TTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttactgctt ... ttttttacagGCCATGTACAATGACTT

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG

      ttttgac  putative branch site (score: 3)
                                        ttatttttttt  putative PPT
                    tttaaactcttattca  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