ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CATATATGAGGATGTTAATCAATCGATTCAGCATGTTCACAGAAGTGGTTTAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATAAAAAAAgtaggtggcaccgtggcacacttttattggttctttaatctggaattttaaatatcaaattatcaatgatctaaccttaagctgcttcttgtttttgacattctttctcatatcttatctctaagactgttgcctaacctgtgacatgcag

Basic information

species	Zea mays
transcript	GRMZM2G040945_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G040945_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g25640.1 (Oryza sativa), 5'ss of exon 6

CATATATGAGGATGTTAATCAATCGATTCAGCATGTTCACAGAAGTGGTTTAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATAAAAAAAgtaggtggca--------ccgtggcacact--------------------tttattggttctttaa----tctggaattttaaatatcaaattatcaatgatctaacctt--aagctgcttcttgtttttgacattctttctcatatctta-tctctaagactgttgcctaacctgtgacatgcag
  ||||||| || || || ||||||||||||||||| |||||||||||| | ||||||||| |||||||||| |||||| |||||| |||||||||||| |||  |  ||         |   ||| | |                    |||     || | |||    | |  | ||||  | | ||     | ||   |||  ||||   |  | | | |  |   ||| |||| ||| |  ||   | ||||| ||||  ||||||    ||||||   |||
TGTATATGAAGACGTAAACCAATCGATTCAGCATGTCCACAGAAGTGGTCTGATTCACAGGAAAATTCTTTCGGAGCCTCAGAAATATCTGATAAAAAATgtacattacaaatattcttctaagcatattgcctttccccctcccctgcatttgccttttttctaattattttttatttttgcagagcagtgctttaacattcttgccttttgactttcgtttattcaatgatattcgttcaccaatgcaactctctgagaccattgccttctatgtgacccacag

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|76915905|gb|DV166160.1|DV166160

EST:     TAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATNNNNNNN                         NGCCAGGTGTTCCGTTTCTTGAAGATGCTGAAAGAGA
genomic: TAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATAAAAAAAgtaggtggca ... tgacatgcagAGCCAGGTGTTCCGTTTCTTGAAGATGCTGAAAGAGA

EST: gi|78103885|gb|DV522308.1|DV522308

EST:     TAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATNNNNNNN                         NGTTAGGTGTTCCGTTTCTTGAAGATGCTGAAAGAGAAAGGGAAAAAGCTA
genomic: TAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATAAAAAAAgtaggtggca ... tgacatgcagAGCCAGGTGTTCCGTTTCTTGAAGATGCTGAAAGAGAAAGGGAAAAAGCTA

EST: gi|71417284|gb|DR803998.1|DR803998

EST:     TAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATNNNNNNN                         NGCCAGGTGTTCCGTTTCTTGAAGATGCTGAAAGAGAAAGGGAAAA-GCTA
genomic: TAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATAAAAAAAgtaggtggca ... tgacatgcagAGCCAGGTGTTCCGTTTCTTGAAGATGCTGAAAGAGAAAGGGAAAAAGCTA

EST: gi|94475337|gb|EB704295.1|EB704295

EST:     TAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATNNNNNNN                         NGCCAGGTGTTCCGTTTCTTGAAGATGCTGAAAGAGAAAGGGAAAAAGCTA
genomic: TAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATAAAAAAAgtaggtggca ... tgacatgcagAGCCAGGTGTTCCGTTTCTTGAAGATGCTGAAAGAGAAAGGGAAAAAGCTA

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: 305

CATATATGAGGATGTTAATCAATCGATTCAGCATGTTCACAGAAGTGGTTTAATTCACAGGCAAATTCTTTCCGAGCCTGAGAAATTTCTGATAAAAAAAgtaggtggca ... tgacatgcagAGCCAGGTGTTCCGTTTCTTGAAGATGCTGAAAGAGAAAGGGAAAAAGCTATTTCTTCTTACTAATTCGCCTTTCTACTTTGTAGATGGAGGGATGCGTT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 106

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 104