ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcag

Basic information

species	Zea mays
transcript	GRMZM2G423861_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G423861_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 9

TCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgat--ctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcag
|||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||| |  ||||||||| ||| ||||||||||| |||||||||||||||||||  || ||||   | || |||    |||   ||||||  |  |  | || || |    ||| ||| | |||||||
TCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATGATCCAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgatgcctaaccacatgttg-aaatgctatacgttttctgccagttttagctaatttctt-tttctgcgttaatgcag

upper sequence: GRMZM2G423861_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 10

TCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaat-gcag--------------------------------
 || || |||||||| || |||||||||||||| || |||||||||||||| || ||| |  | ||||||   || ||  |||| || || || ||||||||  |        ||   ||   ||  |     ||| |   ||  | |||  |||| ||  | ||||  ||  || |||                                 
ACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATGATCCCATTGGACTTTTGCCTGGACGGATCATCTTGGGCATTAATAAGCGAGGGgtgagtcagagttatattattataatgta----tctgtacatt--gcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacag

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|18383721|gb|BM416921.1|BM416921

EST:     GCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGG                         G-TCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA
genomic: GCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA

EST: gi|18649769|gb|BM498588.1|BM498588

EST:     CTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGG                         GTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA
genomic: CTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA

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: 273

TCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 40

Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 43