ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttcacgactggatctcgccggttgattttgcttacattgaaagcgactcgttctgatcccatcgtcttcttctcttttttgtatttctggtggc...

Basic information

species	Zea mays
transcript	GRMZM2G359234_T01
intron #	1
splice site	5'
intron type	U12 (go to U12 genes for details)

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 5'ss of exon 1

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttcacgact-ggatct---cgccggttgattttgcttacattgaaagcgactcgttctgatcccatcgtcttcttctcttttttgtatttctggtggc
|||||| |||||||| ||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||| || |  ||||||   |     ||   |||||||||||| |   ||||| | | |||||   || | |  || | ||| |||  ||  |||    
CGATGTCGTCGAGCCCATCCTGCTCGAGGTGGACCGGATCTATCACCTCGCGTGCCCCGCGTCCCCTGTGCACTACAAGTACAACCCCATCAAGACGATCatatccttctcgtcccggatctgcacatacctttgatttgcttacattcatgtcgacttgatttgatcttctcctttatttttttttattgggttggtgg----

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA10G05260.1 (Glycine max), 5'ss of exon 1

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttcacgactggatctcgccggttgattttgcttacattgaaagcgactcgttctgatcccatcgtcttcttctcttttttgtatttctggtggc------------------
||| || || ||||| || ||  | ||||| || | |||||||||||||||||| ||||||||||| ||||||||||| ||||||||  ||||||| ||||||||||||    ||   |     |   ||| |   | |   || ||       |  |||  |  | |  | || |    ||| |  |   |   |||                    
CGACGTCGTTGAGCCGATTCTGTTGGAGGTTGATCAGATCTACCACCTCGCGTGTCCCGCGTCGCCGGTGCACTACAAATACAACCCCGTCAAGACCATCatatccttcctctctatgttctaact-ctgactcgccgtgtttttaagttccagctctcttttttcgtaattttttatgttttgtgttgaattctgtgatccttaattgttggcttac

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G19640.1 (Glycine max), 5'ss of exon 1

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatcctt--cacga----ctggatctcgccggttgattttgcttacattgaaagcgactcgttctgatcccatcgtcttcttctcttttttgt-atttctggtggc--------
||| || || ||||| || || || |||||||| | |||||| ||||||||||| ||||||||||| ||||||||||| ||||||||  ||||||| |||||||||||  | |||    ||   |||  |     | ||||  | |  |  ||     ||  ||  |      |  | ||    |   || ||| ||   |  |           
CGACGTCGTTGAGCCGATTCTGCTGGAGGTGGATCAGATCTATCACCTCGCGTGTCCCGCGTCGCCGGTGCACTACAAATACAACCCCGTCAAGACCATCatatccttgtctcgatgttctaactctaactcagcgttttttttaagttctaataactcttttttcgtaatttttattttgcgttgagttctgtgatccttaattattagtttac

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 1
lower sequence: PP1S209_52V6.1 (Physcomitrella patens), 5'ss of exon 1

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttcacgactggatctcgccggttgattttgcttacattgaaagcgactcgttctgatcccatcgtcttcttctcttttttgtatttctggtggc----------------------------------------------
|||||| || |||||  |  | || |||||||||| ||| || ||||| ||||| || |||||||| ||||| ||||||| |||||| |||||||| |||||||||||        ||  ||     |||  | |  | |   ||||| |  || |   |  ||| ||     |||    |||| | |  |   |                                                   
CGATGTGGTGGAGCCTTTGTTGCTGGAGGTGGACCAGATTTATCACCTTGCGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATCatatccttttttgtgcgagatc-----ttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcctacac

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 1
lower sequence: PP1S60_124V6.1 (Physcomitrella patens), 5'ss of exon 1

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttcacgactggatctcgccggt--tgattttgcttacattgaaagcgactcgttctgatcccatcgtcttcttctcttttttgtatttctggtggc-
||| || || |||||  || | || ||||| || | |||||||||||| || ||||| || || ||||| |||||||||| ||||||  ||||||| |||||||||||  | ||    ||   | | |  ||||   | || |    |||  | || || | ||    |||     | |  || || ||| | | | ||| | 
CGACGTCGTGGAGCCTCTCTTGCTGGAGGTCGATCAGATCTACCACCTTGCTTGCCCTGCCTCACCTGTCCACTACAAGTTCAACCCTGTCAAGACAATCatatccttttccaccctctcctccagttgatgatcacgttttcgcacaaaatg-cttgt-cagactttatcagag-cgtagctgttgtgtttctgttgtgcct

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 1
lower sequence: PP1S120_28V6.1 (Physcomitrella patens), 5'ss of exon 1

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttcacgactggatctcgccggttgattttgcttacatt--gaaagcgactcgttctgatcccatcgtcttcttctcttttttgtatttctggtggc-
 ||||| ||||| ||  |  | || |||||||||| ||| ||||| || || || || |||||||| ||||| ||||| | ||| ||||||||||| |||||||||||    |  | || | |  | ||    ||  | ||||   ||  |||  |   || ||||   | || |  || |     | ||  ||  |    | 
TGATGTGGTCGAACCCCTTTTGCTGGAGGTGGACCAGATTTACCATCTGGCATGTCCGGCGTCGCCCGTGCATTACAAATTCAATCCAATCAAGACAATCatatcctttcaaa--gaatgttggggtttaccgttaatgacatcaggagggcgggttcgtcagatcatgttgt-tggttgtggcactggtgcttgcgtgctct

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 1
lower sequence: PP1S120_29V6.1 (Physcomitrella patens), 5'ss of exon 1

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttcacgactggatctcgccggttgattttgcttacattgaaagcgactcgttctgatcc-catcgtcttcttctcttttt---tgtatttctggtggc---------------------------
             ||  |  | || |||||||||| ||| ||||| || || || || |||||||| ||||| ||||| | ||| ||||||||||| |||||||||||      | |   ||     || ||| ||  |  |||||       | ||  |  |   ||| ||| |  |  |        |||||   |||| |                            
------------ACCCCTGTTGCTGGAGGTGGACCAGATTTACCATCTGGCATGTCCGGCGTCGCCCGTGCATTACAAATTCAATCCAATCAAGACTATCATATCCTTTTTTgttcgggatcttgaatttattctgaat-tattgagtttatgtagtgttattttgcatagtccttctagcagagagaatgtatccgtggtcgtgcagcctccttgacctgcctccacaag

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 1
lower sequence: EFJ23020 (Selaginella moellendorffii), 5'ss of exon 1

------------CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttcacgactggatctcgccggttgattttgcttacattgaaagcgactcgttctgatcccatcgtcttcttctcttttttgtatttctggtggc
            |||||| || |||||  | || || |||||||| | |||||| ||| | || ||||| |||||||| || |||||||| | ||||||  |||||||||||||||||||  |  ||     |   |      | || |   |||  || |||  |  ||    |  | | |  | |||  || ||     ||||    |  
GCTCATCCGGCACGATGTTGTGGAGCCGCTGCTGCTGGAGGTGGATCAGATCTATCACTTGGCCTGCCCTGCGTCGCCCGTCCACTACAAATTCAACCCGgtcaagacgatcatatccttttcttctttgcttgttcttcgtttctttcgagcatctaacgcgttttttt----tttcgttgcttccttaactcttggagctttcacaag--

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 1
lower sequence: EFJ30517 (Selaginella moellendorffii), 5'ss of exon 2

------------CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttcacgactggatctcgccggttgatt-ttgcttacattgaaagcgactcgttctgatcccatcgt--cttcttctcttttttgtatttctggtggc
            |||||| || |||||  | || || |||||||| | |||||| ||| | || ||||| |||||||| || |||||||| | ||||||  |||||||||||||||||||  |  ||    || |    | | || || |   |||  || |||  |  || |  |    | ||  |||| |    | || |   ||      | 
GCTCATCCGGCACGATGTTGTGGAGCCGCTGCTGCTGGAGGTGGATCAGATCTATCACTTGGCCTGCCCTGCGTCGCCCGTCCACTACAAATTCAACCCGgtcaagacgatcatatccttttcttctttg-cttgttcttcgtttgtttcgagcatctaacgcgtgttttttttttttttttgttgcttccttaactcttggagctttcacaag-

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|32808730|gb|CD960964.1|CD960964

EST:     CGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATC                         AAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATT
genomic: CGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttca ... cactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATT

EST: gi|78125737|gb|DV544121.1|DV544121

EST:     CGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCACTCAAGACGATC                         AAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATT
genomic: CGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttca ... cactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATT

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), 46 (downstream exon)
Score: 105

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttca ... cactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 411