ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtttgtattcagtgtttacagtgttcgtactgataccaattgtaccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT

Basic information

species	Zea mays
transcript	GRMZM2G122935_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g28990.1 (Oryza sativa), 3'ss of exon 5

gtttgtattcagtgtttacagtgttcgtactgataccaattgtaccaata----tgacttg-atta---ttctctgac-cctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
||||   |||||||  |      | | || |   |   |   ||| | ||    | | ||| | ||   || ||  || | | |||||||||  | ||| |  || | ||||| || |||||||| || || |  ||||||||||||||||||||||||||||||||||||||| | |||||||| |
gtttcacttcagtgccttggaattccttatttccatttaaactacaagtaattgtcatttggactaaatttttcaaacacatttcagGAATCTCTAAGGCGTGTTCTCATTATCTTCTCAAAATTAAATCCTACCATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTCTTTTTTATGTGT

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5

gtttgtattcagtgt-ttacagtgttcgtactgataccaattg------------taccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
|||  |  ||  | | ||    | |||| | | || |||| |             | ||| | ||||||     || || |    |  |||||  | || | ||  || |||||| | ||| |||| |||||| |  ||||||||||| | ||||||||||||||||| ||||| ||| | || ||||| |
gttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5

-------------gtttgtattcagtgtttacagt-gttcgtactgataccaattg--taccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
              |||  |||   | || | | |  | |  ||| |  ||  ||   | ||| | ||||||     || || |    | ||||||  | || | ||  || |||||||| ||| |||| |||||| |  ||||||||||||| ||||||||||||||||| ||||| ||| | || ||||| |
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G04830.2 (Arabidopsis thaliana), 3'ss of exon 5

-------gtttgtattcagtgtttacagtgttcgtactgataccaattgtaccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
        ||||| |||    |   ||   ||    ||  |    |||   | ||  | | |    | |    | ||      |||||||  ||| ||  || ||| || ||||| | || || ||||   | || |||||||| ||||||||||| ||| |||| |||||| | ||||||||||
gtaacctttttgtgttct-catcagcaaattttcacctatttttgattaatcaaagctcagtgacatttcgatttacatgtctagGAATCTATGAAGAATATATTACTTGTATTTGCGAAGTTAAACCAAGGCATCAGATATGTTCAAGGGATGAACGAAATTTTAGCACCTATCTTTTATGTAT

upper sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 5

gtttgtattcagtgtttacagtgttcgtactgataccaattgtaccaatatgacttgattattctctgaccctat--cagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
|| ||| ||   |  ||   |  |  |   |||||| ||    ||| || ||||   ||||        |  |||  |||||  | |||||||  || || ||| | ||| |||| ||||| ||  ||||||||||||||||||||||||||||| ||||||| ||| |||| |||||||
gtatgtgtt-gttacttgaggcatgagacttgatacaaacatcacccatttgaccaaattaaatggatcctgtatttcagGATGCTTTGAGGAACATATTGATTGTGTTTGCAAAGTTGAATCCGGGTATAAGATATGTGCAAGGGATGAATGAAATTTTGGCGCCTCTATTCTATGTAT

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|76011673|gb|DT938843.1|DT938843

EST:     TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG                         GAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA
genomic: TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAGgtttgtattc ... accctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA

EST: gi|78110295|gb|DV528710.1|DV528710

EST:     TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG                         GAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA
genomic: TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAGgtttgtattc ... accctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA

EST: gi|76017397|gb|DT944567.1|DT944567

EST:     TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAG                         GAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA
genomic: TAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAGgtttgtattc ... accctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATA

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: 85

GATTCAGAGTTACTAGAACAGATAGACCGAGATGTAAAGCGAACACATCCTGATATTTCATTTTTCTCATCAAAGTCTAACCAGgtttgtattc ... accctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 85

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 124

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 68

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtactgataccaattgtaccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT