ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGCCGCGGCTGTGTGCCCTAGCGGTGGGTCGTGCAGAGTCATTGAAGTTCCACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaagcttggtttgtgtggagtccgtcctcagattttaattttccacctttcaattttactgataaattgttatttctttggttcag

Basic information

species	Zea mays
transcript	GRMZM2G005849_T03
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G005849_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 10

---TGCCGCGGCTGTGTGCCCTAGCGGTGGGTCGTGCAGAGTCATTGAAGTTCCACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttg-------tctaa---gcttggtttgtgtggagtccgt--cctcagattttaattttccaccttt----caattt----tactga-taaattgttatttctttggttcag
    ||  | || || ||||||||   ||| || ||||| || |||||||||||| |||| || |||||||||||||||||||| ||||||||||| |||||||||||       | | |   | ||  |||      | |||    | ||   || |  |||  ||  | |    ||||||    |||||| |   ||||||||| || | |||||
AGACGCATCTGCCGTTTGCCCTAG---TGGATCTTGCAGGGTTATTGAAGTTCCAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacattctttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtgttgttatttgttcg-ttcag

upper sequence: GRMZM2G005849_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os12g03720.2 (Oryza sativa), 5'ss of exon 10

---TGCCGCGGCTGTGTGCCCTAGCGGTGGGTCGTGCAGAGTCATTGAAGTTCCACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa-gcttggtttgt--------gtggagtcc---gtcctcagattttaattttccaccttt----caattt----tactga-taaattgttatttctttggttcag
    ||  | || || ||||||||   ||| || ||||| || |||||||||||| |||| || |||||||||||||||||||| ||||||||||| |||||||||||   |  | |||  ||||         |  | | |     | ||   || |  |||  ||  | |    ||||||    |||||| |  |||||||||| ||   |||||
AGACGCATCTGCAGTTTGCCCTAG---TGGATCTTGCAGGGTTATTGAAGTTCCAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacattgtttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtattgttatttgttcc-ttcag

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|7216484|gb|AW562606.1|AW562606

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

EST: gi|89248870|gb|DY620656.1|DY620656

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTGGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

EST: gi|148955139|gb|EC900656.2|EC900656

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTGGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

EST: gi|71771453|gb|DR969390.1|DR969390

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

EST: gi|149005283|gb|EE039832.2|EE039832

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

EST: gi|74242021|gb|DT649935.1|DT649935

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

EST: gi|211029256|gb|FL478423.1|FL478423

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

EST: gi|86855990|gb|DY307001.1|DY307001

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCCCGCGTACCATCTGACTGTTCTCCAGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

EST: gi|149014771|gb|EE044463.2|EE044463

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

EST: gi|113842557|gb|DW969340.1|DW969340

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTACTCCGGGGATTCG
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTT-CTCCGGGGATTCG

EST: gi|111197488|gb|EE295623.1|EE295623

EST:     CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAG                         TTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA
genomic: CACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCA

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: 47 (upstream exon), 43 (downstream exon)
Score: 58

TGCCGCGGCTGTGTGCCCTAGCGGTGGGTCGTGCAGAGTCATTGAAGTTCCACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttgtctaa ... tttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCAAGGAATCTGGCGAAGAGCGTGACCACGCAGTAGGGAGAGGTAGATGAGA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 102

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109