ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGTTTTTCTGGCCAGCGGTTTTATGATGACTGGTTTCAGTCTCTATATAACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggattattcttacttgtttatggagttgtctcctgcaattgcactaagctctgagtcgtttcag

Basic information

species	Zea mays
transcript	GRMZM2G020553_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G020553_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g27220.1 (Oryza sativa), 5'ss of exon 8

TGGTTTTTCTGGCCAGCGGTTTTATGATGACTGGTTTCAGTCTCTATATAACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggat-----tattcttacttgtttatggagttgtctcctgcaattgcactaagct---ctgagtcgtttcag
||||||||| || ||||| ||||||||||||||||| ||||| || ||||| || ||||| || || |||||||||||||| ||||||||||||||||||||| |       ||||| |   |  |||||||||   ||  |     |||| ||  ||   ||||  | ||||||
TGGTTTTTCCGGTCAGCGATTTTATGATGACTGGTTCCAGTCCCTTTATAATGTCATTTTCACGGCCCTACCTGTAATTATGGTTGGATTGTTTGATAAGgtatgtaacttgtattcatttctacttatggagtatactattctctgtgcattacacttaactgatccctttcag

upper sequence: GRMZM2G020553_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G16990.1 (Glycine max), 5'ss of exon 16

-TGGTTTTTCTGGCCAGCGGTTTTATGATGACTGGTTTCAGTCTCTATATAACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggat---tattcttac--ttgtttatggagttgt-ctcctgcaattgcacta-agctctgagtcgtttcag---------------------------------
 ||| |||||||| ||| | || |||||||| |||||||||||  ||||||| ||||| || || || || |||||||| || |||||||| ||||| ||||||||||   | |||  ||  ||  || || |||||| || |     || || || || | |   || |    |                                 
CTGGGTTTTCTGGTCAGAGATTCTATGATGATTGGTTTCAGTCATTATATAATGTTATCTTCACAGCACTTCCTGTAATCATTGTTGGATTATTTGACAAggtaggatatttgttccaacagttacttttgcagttgtgcttcacttgttacattacagtttttcttcatggatggcatgttttgattagtttcttgtgcctttgcca

upper sequence: GRMZM2G020553_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S87_152V6.1 (Physcomitrella patens), 5'ss of exon 24

TGGTTTTTCTGGCCAGCGGTTTTATGATGACTGGTTTCAGTCTCTATATAACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggat-------tattctt-----acttgtttatggagttgtctcctgcaattgcactaagctctgagtcgtttcag---------------------
 || ||||| ||||| || ||||||||||||||||||||||| || || || ||| | || || || || || || ||  | |||||  | || ||  |||||   |       | ||| |     | |||||   |  |        ||  ||| |   |     ||| | | ||  |                     
GGGATTTTCGGGCCAACGTTTTTATGATGACTGGTTTCAGTCCCTCTACAATGTTCTCTTCACCGCTCTTCCAGTGATCGTTGTTGGTATCTTCGACCAGgtaatgtagtcatttgttcctttgatatttgttcgagcggactgacgttgtgattccttcatatcttgacttgattaggttaggtgttggtttaccagga

upper sequence: GRMZM2G020553_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ31523 (Selaginella moellendorffii), 5'ss of exon 24

TGGTTTTTCTGGCCAGCGGTTTTATGATGACTGGTTTCAGTCTCTATATAACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggattattcttacttgtttatggagttgtctc-ctgcaattgcactaagctctgagtcgtttcag
||||||||||||||| ||||| || || ||||||||||||||| |||| || ||  | || || || || || || ||  | |||||| | || ||  |||||          |||||   | ||      | || | |   |||    | ||               
TGGTTTTTCTGGCCAACGGTTCTACGACGACTGGTTTCAGTCTTTATACAATGTGTTGTTCACAGCACTGCCAGTCATCGTTGTTGGAATTTTCGACCAGgtaaccgatacactacttcgctctgtttcattttcacggtgtttgtttgaggcag-------------

upper sequence: GRMZM2G020553_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ38622 (Selaginella moellendorffii), 5'ss of exon 24

TGGTTTTTCTGGCCAGCGGTTTTATGATGACTGGTTTCAGTCTCTATATAACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggattattcttacttgtttatggagttgtctc-ctgcaattgcactaagctctgagtcgtttcag
||||||||||||||| ||||| || || ||||||||||||||| |||| || ||  | || || || || || || ||  | |||||| | || ||  |||||          |||||   |  |      | || | |   |||    | ||               
TGGTTTTTCTGGCCAACGGTTCTACGACGACTGGTTTCAGTCTTTATACAATGTGTTGTTCACAGCACTGCCAGTCATCGTTGTTGGAATTTTCGACCAGgtaaccgatacactacttcgctccgtttcattttcacggtgtttgtttgaggcag-------------

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|67034835|gb|CO463368.1|CO463368

EST:     ACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAG                         GATGTTAGCGCGTCACTGTCNNNNNNNTACCCACAGCTTTACAAGGAAGGC
genomic: ACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggattat ... gtcgtttcagGATGTTAGCGCGTCACTGTCAAAAAAATACCCACAGCTTTACAAGGAAGGC

EST: gi|213170626|gb|FM190014.1|FM190014

EST:     ACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAG                         GATGTTAGCGCGTCACTGTCNNNNNNNTACCCACAGCTTTACAAGGAAGGC
genomic: ACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggattat ... gtcgtttcagGATGTTAGCGCGTCACTGTCAAAAAAATACCCACAGCTTTACAAGGAAGGC

EST: gi|211234536|gb|FK968393.1|FK968393

EST:     ACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAG                         GATGTTAGCGCGTCACTGTC--AAAAATACCCACAGCTTTACAAGGAAGGC
genomic: ACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggattat ... gtcgtttcagGATGTTAGCGCGTCACTGTCAAAAAAATACCCACAGCTTTACAAGGAAGGC

EST: gi|60351278|gb|DN218251.1|DN218251

EST:     ACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAG                         GATGTTAGCGCGTCACTGTCNNNNNNNTACCCACAGCTTTACAAGGAAGGC
genomic: ACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggattat ... gtcgtttcagGATGTTAGCGCGTCACTGTCAAAAAAATACCCACAGCTTTACAAGGAAGGC

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: 45 (upstream exon), 49 (downstream exon)
Score: 89

TGGTTTTTCTGGCCAGCGGTTTTATGATGACTGGTTTCAGTCTCTATATAACGTTATTTTTACTGCGCTACCTGTAATTATAGTTGGATTGTTTGATAAGgtaggattat ... gtcgtttcagGATGTTAGCGCGTCACTGTCAAAAAAATACCCACAGCTTTACAAGGAAGGCATCAGGAATTCATTCTTCAAGTGGAGAGTGATTGCAGTGTGGGGTTTCT

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 93

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106