ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAACTGCCCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgatctgccttttgctcttaattcatgtcctattagggttctattttttatctaaagtttttaaatgaattctattgcattttgcag

Basic information

species	Zea mays
transcript	GRMZM5G826714_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G826714_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 2

CCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAACTGCCCAACATGCTCATGTGGCTGCCAGAAC------CCAAGTGGGTCAAACTGTGTGAAgtgagttgatctgccttttgctcttaattcatgtcctattagggttctattttttatctaaagtttttaaatgaattctattgcattttgcag
      |||||||||| ||||| |||||||||||||||||||||||||||||||||||||| ||||||||||| |||       |||||     || |||||| ||||||||| ||    |     |||||| |||   || | ||  ||  | | ||||  |  ||| ||  |||   | ||| ||    ||   |||
------GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttc-tgcaaaattgctaa-caagttccatgcatttccacag

upper sequence: GRMZM5G826714_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 5'ss of exon 4

CCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAACTGCCCAACATGCTCATGTGGCTGCCAGAAC--CCAAGTGGGTC----AAACTGTGTGAAgtgagttgatctgccttttgctcttaattcatgtcctattagggttctattttttatctaaagtttttaaatgaattctattgcattttgcag
      |||||||||| || || ||||| |||||||||||||||||||||||||||||||| ||||||||||| |||          |||     | |||||| |||||||||  |  || | ||  | ||| ||||                                                              
------GTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACTAGTCCTGGGAGCTGTGTAAAgtgagttactaagc-tgttattgttatttcag-------------------------------------------------------------

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|32831333|gb|CD971011.1|CD971011

EST:     CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         TGAGGATTCACCTAATCTACAAGCTGCAATTGATGGTCCTGGCAAATGGAC
genomic: CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC

EST: gi|45568055|gb|CK985879.1|CK985879

EST:     TCATGTGGTTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         TGAGGTTTCACTTAATCTACAAGCTGCAATTGATGGTCCTGGCAAATGGAC
genomic: TCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC

EST: gi|211426448|gb|FK948042.1|FK948042

EST:     CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         TGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC
genomic: CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC

EST: gi|50332123|gb|CO527249.1|CO527249

EST:     CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         TGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC
genomic: CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC

EST: gi|5847499|gb|AW000578.1|AW000578

EST:     CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         TGAGGATTCACCTAATCTACAAGCTGCAATTGACGGTCCTGGCAAATGGAC
genomic: CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC

EST: gi|91871212|gb|EB401300.1|EB401300

EST:     CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         TGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC
genomic: CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC

EST: gi|32836940|gb|CD976618.1|CD976618

EST:     CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         TGAGGATTCACCTAATCTACAAGCTGCAATTGATGGTCCTGGCAAATGGAC
genomic: CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC

EST: gi|211426451|gb|FK948045.1|FK948045

EST:     CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         TGAGGATTCACCTAATCTACAAGCTGCAATTGATGGTCCTGGCAAATGGAC
genomic: CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC

EST: gi|32846222|gb|CD985903.1|CD985903

EST:     CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         TGAGGATTCACCTAATCTACAAGCTGCAATTGATGGTCCTGGCAAATGGAC
genomic: CCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGAC

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), 48 (downstream exon)
Score: 171

CCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAACTGCCCAACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagttgat ... cattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGACTGGTCAGCCCCTTGTACAATGCACTTCCCACATGTGCCCGATAAGAATC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231