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

gtaatctcttaacttcatgccatgtgcaaatcgatctcagccatgtgcacttaatgttcttatatgttttgctcctcagATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTGGGTGGAAATGTTTGAGGATGTCCGCATGGTGATATTCTCTGTAGCCCTC

Basic information

species	Oryza sativa
transcript	LOC_Os11g10050.1
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os11g10050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G016858_T01 (Zea mays), 3'ss of exon 7

---gtaatctcttaacttcatgccatgtgcaaatcgatctcagccatgtgcacttaatgttcttatatgttttgctcctcagATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTGGGTGGAAATGTTTGAGGATGTCCGCATGGTGATATTCTCTGTAGCCCTC
    |||| |||||||||   ||| |||| |  |   |   |   |||    || |||  | |  | | ||||  || ||||||||||| |||| ||||| ||||| || |||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||||| |||||| |||
gtaataatttcttaactt---gccttgtgaacgtgtgtaaaaaaaatgcat-ctgaatcatgtgctcttttttattcatcagATATCAGCTGATCAGAGTCAGTGCAAAAGGCATGAATGATGGCTGCAAATGGGTGGAAATGTTTGAAGATGTCCGCATGGTAATATTCTGTGTAGCACTC

upper sequence: LOC_Os11g10050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G34300.1 (Glycine max), 3'ss of exon 8

--------------------gtaatctcttaacttcatgccatg-----tgcaaatcgatctcagccatgtgcacttaatgttcttatatgttttgctcctcagATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTGGGTGGAAATGTTTGAGGATGTCCGCATGGTGATATTCTCTGTAGCCCTC
                        || |   || |||| |  ||     |  |||  ||  | ||  | |   |    |    ||| | || | |    | ||| |||||  | || || || | |||||||||| ||||||| |||||||||||||| |||||||| || || || ||    ||| | || | |||  |||| 
ttgctatcaccattgccctcaccttccccccacctcatacactgaaatttagaaactgaaatgagaaacgcaaagactaaacccttctttgatgt----cccagGTATCAACTCATAAGGGTGAATGCCAAGGGCCTGAATGAGGGCTGCAAGTGGGTTGAAATGTTCGAAGACGTTCGAGCAGTGGTCTTTTGTGTTTCCCTA

upper sequence: LOC_Os11g10050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 7

--------------------gta-atctcttaacttcatgccatgtgcaaatcgatct-cagccatgtgcacttaatgttcttatatgttttgctcctc-agATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTGGGTGGAAATGTTTGAGGATGTCCGCATGGTGATATTCTCTGTAGCCCTC
                     ||  ||||||   ||  |  ||| ||  | | ||| |     |||| | | | |   |   |  ||||| || |   | ||||| ||  | || || |||| || |||||| ||||  || || ||||||||||||||||||||||| ||||| ||    ||  | |||| |||  |||| 
atcctgcttctcacttcctactatgtctcttttgtttctctcat-tgggatttgatttatgatcatg-gaattgagaatgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA

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|58611654|gb|CK039366.1|CK039366

EST:     TCTGAGCCTTACATTGAG-AGCGTGAAGCACATTCCCAGCCTCTTACCAA                         ATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTG
genomic: TCTGAGCCTTACATTGAGAACCCTGAAGCACATTCCCAGCCTCTTACCAAgtaatctctt ... tgctcctcagATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTG

EST: gi|87006860|gb|CI285894.1|CI285894

EST:     TCTGAGCCTTACATTGAGAACCCTGAAGCACATTCCCAGACTCTTACCAA                         ATATCAGTTGATTAGAGTAA-TGCCAAGGGCATGAATGAT
genomic: TCTGAGCCTTACATTGAGAACCCTGAAGCACATTCCCAGCCTCTTACCAAgtaatctctt ... tgctcctcagATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGAT

EST: gi|4714818|gb|AU055935.1|AU055935

EST:     TCTGAGCCTTACATTGAGAACCCTGAAGCACATTCCCAGCCTCTTACCAA                         ATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTG
genomic: TCTGAGCCTTACATTGAGAACCCTGAAGCACATTCCCAGCCTCTTACCAAgtaatctctt ... tgctcctcagATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTG

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: 68 (upstream exon), 73 (downstream exon)
Score: 28

GGAATGGGTTGGCTTTCATTGAATTCGCCCTTGATGATCGCAGTCCCATGTCTGAGCCTTACATTGAGAACCCTGAAGCACATTCCCAGCCTCTTACCAAgtaatctctt ... tgctcctcagATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTGGGTGGAAATGTTTGAGGATGTCCGCATGGTGATATTCTCTGTAGCCCTC

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaatcgatctcagccatgtgcacttaatgttcttatatgttttgctcctcagATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTGGGTGGAAATGTTTGAGGATGTCCGCATGGTGATATTCTCTGTAGCCCTC

                        acttaat  putative branch site (score: 28)
                                          ttttgctcctc  putative PPT
                          ttaatgttcttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctcttaacttcatgccatgtgcaaatcgatctcagccatgtgcacttaatgttcttatatgttttgctcctcagATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTGGGTGGAAATGTTTGAGGATGTCCGCATGGTGATATTCTCTGTAGCCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG