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

...tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT

Basic information

species	Oryza sativa
transcript	LOC_Os01g62244.3
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G007300_T02 (Zea mays), 3'ss of exon 4

tatgtttatcttctctagctttttgtaagtagccattttttac-tgtctaatcat-catattcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT
    |  |   |   | | |||    | |||    |||  |   ||  || |  |  ||  |     |  |||| |  || || | |||| ||||||| |||||||| ||||||||||||||||| || || ||||| ||| |||||||||| || ||  ||||||| ||||| ||||||
--gatacagaatgctttgttttggtcaggtacttctttcatgtgtgagtacttttgtatgctatcactagttgttaagttgattattgttatccatttgcagGTTGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGACGAGTCTGCAGCAAACATTGAGGCAGCT

upper sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4

tatgtttatcttct-ctagctttttgta-agtagccattttttactgtctaatcat-catattcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT
   |  || ||||  |||| |   |  | | |   |  | || | ||   | |  |  ||  |     |  |||| |   | |||| |||| | ||||| ||||| || ||||||||||||||||| || || ||||| ||| ||||||||||||| || |||||||| ||||| ||||||
---gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgcatttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT

upper sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G06960.1 (Glycine max), 3'ss of exon 4

--tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcata---ttcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT
   ||| | ||    | | |         || |    || | |||| |  | |  | |||   || || | || ||  || ||||    |||| ||   || ||||| ||||| |||||  |||| ||||| |||||||||||  | || ||||||||||| || |||||| ||||||| || 
gaaatggt-attgcattttgtccaccactagcaaat-ttatatacttttcacttgttataagttttctaagtcatgatatattaaaatatgttatc---ttgcagGTAGAGAGTATAGTATTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCA

upper sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 4

---tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccat-ttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT
   ||||  | |  |      |   || |   | | |||  |    |||  |    |   |  ||||   ||| | | || |     | | | |  | || ||||| ||||| |||||  | || ||||| |||||||||||| |||| ||||||||||| || |||||| ||||||| || 
tgatatgcgtcttcttgtccaccgcttttggtttgacatagta-gttgtaaagctgtttaaaacctg---cttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCG

upper sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4

---tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccat-ttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT----------------------
   | ||    |  |      |   ||||   | | |||  |    |||  |   ||   |  ||||   ||| | | || |     | | | |  | || ||||| ||||| |||||  | || ||||| |||||||||||| |||| ||||||||||| ||||||||| ||||||| ||                       
gtttttgccacttcttgtccaccacttgtggtttgacatacta-gttgtaaagctatttaaaacctg---cttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT

upper sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4

---tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccat-ttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT
   | ||    |  |      |   ||||   | | |||  |    |||  |   ||   |  ||||   ||| | | || |     | | | |  | || ||||| ||||| |||||  | || ||||| |||||||||||| |||| ||||||||||| ||||||||| ||||||| || 
gtttttgccacttcttgtccaccacttgtggtttgacatacta-gttgtaaagctatttaaaacctg---cttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG

upper sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G59300.1 (Arabidopsis thaliana), 3'ss of exon 4

---------------------------------------------------------tatgtttatcttctctagctttttg----taagtagccattttttactgtctaatcatcatattcctgat--tcttgtaattttaatgagtgttttc-catttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT
                                                         |||| |||   |  |||   ||  |    ||   ||  || | |   ||  | ||  |||| |  | |||  || ||   |  | |      || |     || ||||||||||| ||  |  |||| ||||| || |||||||||||||| || ||||| || ||||||||| ||||||| || 
gtatgttcaaattgatttgagtttgttcatttttgttcgcttcatagtagtagattctatgattagagttactatagttcagacactataaagggatctctaggtgatttatt-tcatgtctcagatgttcatgccgtagtgaaacaaattatggtgctttcagGTTGAGAGTATTATGTTGAGTATCATATCAATGCTTTCTGGTCCTAACGATGAGTCTCCAGCAAATGTTGAAGCTGCC

upper sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 4

tatgtttatcttctctagctttttgtaagtagccattt---tttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT
 || ||       |  || |  | ||  || | || ||   ||  || ||||   | ||||||  ||   |||  || | |    | || | |    | ||||||||| || |||||| |||| ||||| |||||||||||  | || |||||||||||||| ||||| |||||||| || 
-atattatagagtttaaggtcatcgtgtgttgacaattattttccctatctagcgaccatattaatg-cacttacaactattgc-attgatgttatgtcacagGTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA

upper sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 4

tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT
 |     ||  | | ||   ||| | |    | |||   ||    |    |  |  ||||     ||    |  | ||| || |    || ||  | |||||||| ||||||||| |||| ||||| || ||||||||  |||||||||||||||| || |||||||||||||| |||
gaaaaagatactgtatattatttggcatactgacatcacttttgattcccttttggtatttgctttttgacttttattactgggatggtttcacatgcagGTTGAAAGCATAGTTTTGAGTATCATATCAATGCTTTCAAGTCCAAATGATGAATCTCCTGCAAATATTGAAGCTGCT

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|33656879|gb|CF279493.1|CF279493

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTTTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|33682529|gb|CF310768.1|CF310768

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|33693886|gb|CF322125.1|CF322125

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|9866226|gb|AU101976.1|AU101976

EST:     CCCCAATGGTTNTGAGCTTGCGAGTGAGCNTTGGACACCCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: -CCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACA-CCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|86421652|gb|CI057641.1|CI057641

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|218503159|gb|FG952517.1|FG952517

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|88994676|gb|CI036257.1|CI036257

EST:     GTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCCAATGAT
genomic: GTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|218489286|gb|FG970461.1|FG970461

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|88985016|gb|CI011872.1|CI011872

EST:     TTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: TTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|15846873|gb|BI795149.1|BI795149

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|8860110|gb|AU097428.1|AU097428

EST:     TCCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: T-CCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|2800997|gb|AA754291.1|AA754291

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGMCAC-AGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGCCCAAATKAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|58589723|gb|CF988031.1|CF988031

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|86870070|gb|CI317991.1|CI317991

EST:     ATCCCAATGGTTATTAGC-TGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTTAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|33655964|gb|CF278578.1|CF278578

EST:     GTTATGAGCTTGCGAGTGAGCGTTGGACACCCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: GTTATGAGCTTGCGAGTGAGCGTTGGACA-CCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|33811991|gb|CF331885.1|CF331885

EST:     ATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTTTGGTCCAAATGAT
genomic: ATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|33803962|gb|CF327857.1|CF327857

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|33687165|gb|CF315404.1|CF315404

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

EST: gi|88979399|gb|CI025901.1|CI025901

EST:     ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACG                         GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT
genomic: ATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGAT

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: 70 (upstream exon), 74 (downstream exon)
Score: 39

TTATCCGGATGGACGTGTATGCATTTCTATTCTTCATCCGCCTGGTGATGATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATACGgtacgaatta ... ccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tctaatcatcatattcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT

                             ttttaat  putative branch site (score: 39)
                                         ttttccattt  putative PPT
                   attcttgtaattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccatttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - tttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcttg