ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgacattttagttccgtttcttttcgtatacaatgtcacttaatcttgtgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

Basic information

species	Oryza sativa
transcript	LOC_Os07g48820.2
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3

gtgacattttagttccgtttcttttcgtatacaatgtcacttaatcttg--tgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
|| | ||  | ||||| |||  |   || |   || | || |  | |||  ||| ||||||| ||| ||  | |||  |||    |||||||| || |||||||| ||||||||||||||||||||||||||||||||||||||||||
gtaatatcgtggttcctttttctcaagt-tcttatttaaccttgtattgcttgttattaattgcatttttgaatttt-catatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

upper sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G31050.3 (Glycine max), 3'ss of exon 6

gtgacattttagttccgtttcttttcgtatacaatgtcacttaatcttgtgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
      || || | | ||   | |  | | | |   | |     | ||||     |    | || ||  |||||  ||| ||   |||| |  | ||||||||||||||||||||||| || || ||||| || ||||||||||||
-----gttgta-tgcagtaattgtgtgcaaatagcataagcc--ttttgttactgtgtgctaatttttcattttt-cattca---gACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4

-------------gtgacattttagttccgtttctt---ttcgtatacaatgtcacttaatcttgtgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
                  ||||||  |  | || |    ||  |||  ||  |   | |||  | | || |||  |   |||||  ||||    |     ||||  | ||  |||||||||| ||||||||||||||||||||||||||| |||| || || 
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaatt-ttaaatggtatttg-ttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA

upper sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G28400.1 (Glycine max), 3'ss of exon 1

---------gtgacattttagttccgtttcttttcgtatacaatgtcacttaatcttgtgtgatta---atttcatattgtattttggcatgcaat--agACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
            |   || | | | ||   | |    | |     | |   |  ||| ||| | ||   |||   | || | ||||    |   ||  ||||| |  | ||||||||||||||||||||||| || || ||||| || |||||||||| |
ttgaccaatcaaaaggttaaatgcagtaattgtgttcaaatggcataagcaagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAATG

upper sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6

gtgacatttta-gttccgtttcttttcgtatacaat--gtcacttaatcttgtgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
      || || |      || | |||  ||   ||  | |  ||  |  | ||   | | |||  | || |  |||  ||| ||   |||| |  | ||||||||||||||||||||||| || || ||||| || ||||||||||||
-----gttgtatgcagtaattgtgttcaaatggcataagccttttgttactatgcattaatttttctttttttatttttcattca---gACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

upper sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G44270.1 (Glycine max), 3'ss of exon 4

--gtgacattttagttccgtttc---ttttcgtatacaat-gtcacttaa--tcttgtgtg--attaatttcat----attgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
     | || ||   ||  |||    ||||  ||| |  |  |||  |||  | ||   ||  |||  || |||    ||||  ||||    |     |||   | ||| |||||||||| ||||| ||||| ||||||||||||||| |||| || || 
aaaacaaatgtttactctattttaaattttgttatgcggttatcatctaaaattttaaatggtatttgttacatgatcattgattttttaattattgcagAGTCTCCGGAGGCTTGCTCAGAATCGCGAGGCTGCAAGAAAAAGTCGGTTGAGAAAGAAA

upper sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4

gtgacat-tttagttccgtt--tcttttcgtatacaatgtcacttaatcttgtg--tgattaatttcatattgtattttggcatg--caatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
|||| |  || |  || ||   ||   | | || |  |||   |||  | | ||  | ||   |||  | ||   ||| |   ||  | ||||||  ||||  ||||||||||||||||||||||||||||||||||  |  ||||||| |||
gtgatagattcatctctgtggatcaactagcat-ctgtgtatattacgcatatgcataatctgttttgt-ttccttttcgttttgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG

upper sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 3'ss of exon 4

gtgacattttagttccgtttcttttcgtatacaatgtcacttaatcttgtgtgattaatttcatattgtattttggcatg-----caatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG
||||||| |   |  | | |   |  |   ||  | |   || | |   | |   |||| || | |||| |  |   ||      | ||||||  ||||  ||||||||||||| |||||||||||||| |||||  |  ||||||| |||
gtgacatgtccatctc-tgtagataagatcactgtttttattcagccaattta--taatctctttttgtttccttatattttgatccatagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG

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|29639367|gb|CB644376.1|CB644376

EST:     CTAACTCTTCAGATAGATCTGACAGATCTGACAAACTTATGGACCAAAAG                         ACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTG
genomic: CTAACTCTTCAGATAGATCTGACAGATCTGACAAACTTATGGACCAAAAGgtgacatttt ... catgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTG

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 1 RNA-Seqlibrary.

Block sizes: 66 (upstream exon), 60 (downstream exon)
Score: 30

TTAGAAAACGGACATAGTGGTGCAGTCATGGCTTCTAACTCTTCAGATAGATCTGACAGATCTGACAAACTTATGGACCAAAAGgtgacatttt ... catgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

caatgtcacttaatcttgtgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

                     gattaat  putative branch site (score: 30)
                    tgattaatttcatatt  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

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacattttagttccgtttcttttcgtatacaatgtcacttaatcttgtgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA