ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactcgcagtgtaatgtctccatccaaatatcagacatcc...

Basic information

species	Zea mays
transcript	AC209208.3_FGT002
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g44630.3 (Oryza sativa), 5'ss of exon 2

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactcgcagtgtaatgtctccatccaaatatca--gacatcc-----
|||||| |||||||||||||| || || ||||||||||||||||| ||||||||||||||||||||||||||||||| ||| || |||||||| |||||||||||   |||   |||    || | | | ||| |||  || ||  |  || || ||| || ||  || | | |  | |   ||   | ||||  || |  |     
CCACCTGGCCACCATCCCCATCACCGGTACTGGCATCAACCCAGCCAGGAGCCTTGGCGCTGCCATCATCTACAACAAGGACCATGCCTGGAATGACCATgtgagc--aacctttct----tctctttttacctactcgccgttctcagcaatt-ggttcctcttacattatcagatattagtcagcacatcattgataatcgatac

upper sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G01860.1 (Glycine max), 5'ss of exon 3

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaact-actctcgattcccctctaaccaactttccatttcc-tacagtttggtaccactcgcagtgtaatgtctccatccaaatatcagacatcc
|||| | || ||||| ||||| || || |||||||| |||||||||||||| || || |||||||||||||||||||| || || || ||| | ||||| ||  ||     | |  || || |      |    |  || |||||  | ||     |  |   | | |   | |    | |   |  || ||||  ||    
CCACTTGGCTACCATTCCCATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttttttgagacttgaatttttgtttcatatattcccattagcataggaaataatgtaaatagttttattgaattttattataattatcttaccg--

upper sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 3

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactcgcagtgtaatgtctccatccaaatatcagacatcc
|||| | || ||||| || || || || |||||||| |||||||||||||| ||||| ||||| || || |||||||| || || || ||| | ||||||||   |  |  | || ||      | | |   |  ||||   || | |  |  |   |     |  | || |||| | |   |     |  |||      
CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgtatatacatgtcctttca-----cttatgtgcctctttgttttgcatgaaagtgactttatttaactgtttaat-tttaattgtggcttacag------

upper sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G37730.1 (Glycine max), 5'ss of exon 3

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactcgcagtgtaatgtc---tccatccaaatatcagacatcc------
|||| | || ||||| ||||| || || |||||||| |||||||||||||| || || |||||||||||||||||||| || || || ||| | ||||| ||  ||        |||   ||||  | |||   |||||  ||||  |    | |  | ||| | |||  | ||  |    |  ||    ||||      |        
CCACTTGGCTACCATTCCCATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgt-------ttcttacttcctttttaa--gactttaaattttgttacatatattcccattagcataggaaaataaggtaaatagttatattgatttttataataa

upper sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 3

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactact-ctcgattcccct-ctaaccaactttccatttcctacagtttggtaccactcgcagt-gtaatgtctccatccaaatatcagacatcc-
 || || || ||||||||||| || || || ||||||||||| |||||||| || || || |||||||||||||||||||   | |||||| | |||   || |||| ||  | | ||| ||       |  |  | |||  ||| || | ||  |   |   | ||  | | ||| ||  | ||| |   |      ||||  
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTCGGGGCCGCCATCATCTACAACAGGGGGAATGCCTGGGATGACATGgtaagtgaaaacattgctctataagaagacccaatagcttctcatctcgt-catctatctgtgaatctgacttgtattgatttcattcttgttgttcccatcag

upper sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactc-gcagtgtaatgtctccatccaaatatcagacatcc---
 || || || ||||||||||| || || || ||||||||||| |||||||| || || || ||||||||||||||||| || || |||||| | |||   || ||        |||     ||    | || || |||  ||| || | || ||   |   | || ||  |||| ||  | ||| |   | |    |       
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaag--------ctccatgatcagacccaatca-cttctcatctcat-catttatctgtgaatctgccttgtattgatttcattcttttgttgttcccttcag

upper sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0067g00220.t01 (Vitis vinifera), 5'ss of exon 3

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactcgcagtg--taat-gtctccatccaaatatcagacatcc---------------------------
 ||| | |||||||||||||| ||||| || ||||||||||||||| ||||||| || || |||||||||||||||| ||| ||||| ||| ||||||| || ||    ||   | | |  | | ||    |    ||||| || |||    ||     | |||| || |    ||| ||    || |  ||    | | |                             
GCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTGCGGCCATCATCTACAACAAGGACCACGCATGGGACGACCACgtaagcc--accgat-tgggcttctctacttcattttttcctttcccttttcttctagtcaactcacaataatcaatagtgctaatgcttatggttgccttttcttttcttttactgcctcatgctacag

upper sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 5'ss of exon 3

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtgg------aactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactcgcagtgtaatgtctccatccaaatatcagacatcc--------
 ||| | |||||||||||||| || || |||||||| |||||||| ||||| ||||| ||||| ||||||| |||||| || || || ||| | |||   ||  |||        |  |      |       ||||  || ||| |||    |   | ||      | |  ||||  ||  |||   |   | | |    |            
TCACTTGGCCACCATCCCCATCACAGGAACTGGCATTAACCCAGCCAGGAGTCTTGGAGCTGCTATCATCTTCAACAGAGAGCATGCATGGGATGACATGgtaggtgttttgatgagaaaaaaaaaaaaaaacctaaggaattttgcatcctttgatggttaaattgagtttcagttcaagttcttattgtgactttttttctcttgctttcag

upper sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
lower sequence: EFJ18960 (Selaginella moellendorffii), 5'ss of exon 3

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactcgcagtgtaatgtctccatccaaatatcagacatcc
|||||||||||| |||||||| |||||||| ||||||||||||||  | || || ||| | ||  ||||||||||  | || || |||||| | || ||||| ||    |  |||     || | || | |     |  |  ||   |  ||||         |    ||| |  ||||   |  ||  |          
CCACCTTGCCACGATCCCCATCACTGGCACGGGCATCAACCCAGCGCGAAGTCTCGGCTCGGCTGTCATCTACAATGGCGACCAGGCCTGGGATGATCATgtaag----atcact-----ttactctttgaatttttcgctcttcttttaagttctaacttgtt---ggtgcatcgtctgtgtgtaagcag---------

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|149094560|gb|EE180082.2|EE180082

EST:     GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCAT                         TGGATCTTCTGGGTCGGCCC
genomic: GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCC

EST: gi|213172229|gb|FM182804.1|FM182804

EST:     GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCAT                         TGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCCCTGGCTGCCATCTAC
genomic: GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTAC

EST: gi|148982069|gb|EE028110.2|EE028110

EST:     GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCAT                         TGGATCCTCTGGGTCGCCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTA
genomic: GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTA

EST: gi|149046894|gb|EE048104.2|EE048104

EST:     GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCAT                         TGGATCTTCTGGGTCGGCCCC
genomic: GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCC

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 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 525

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 674

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 944