ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCCTCATGGCTTAGCTGAGGGATGGAAATGGCTCGCCATGTTCCTCAATTCTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatctgcttcaagacctcctgtttgcgtgccattagttaatcggggttcttatgcttttcag

Basic information

species	Zea mays
transcript	GRMZM2G417217_T03
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G417217_T03 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g38250.1 (Oryza sativa), 5'ss of exon 14

TCCTCATGGCTTAGCTGAGGGATGGAAATGGCTCGCCATGTTCCTCAATTCTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatctgcttcaagacctcc---------------tgtttgcgtgccat----------tagttaatcggggttcttatgcttttcag
||| ||||||||||||||||| ||||||||||| ||||||||||| ||| |||| || || || ||||| ||||||||||||||||| || ||||||||||||  ||| |||||||||||| ||               ||| ||| ||              |||  ||   || ||||  | || |||||
TCCACATGGCTTAGCTGAGGGGTGGAAATGGCTTGCCATGTTCCTTAATACTCTCCCGGCCACCACAGCAACTGCTTGTGCCCTTCATGCTTTCCTCAAGgtaaaaatatgcttcaagacccccatcccctcctatgcgtgtgtgcttgtagcaggtttgttgtagccaacttggattctgtttctgttcag

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|31355428|gb|CD439785.1|CD439785

EST:     CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAG                         ATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
genomic: CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatct ... tgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC

EST: gi|67016820|gb|CO445569.1|CO445569

EST:     AGCCACTGTTTGTGCCCTTCACGCCTTCCTCAAG                         A-GGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
genomic: AGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatct ... tgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC

EST: gi|24769979|gb|CA405108.1|CA405108

EST:     CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAG                         ATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
genomic: CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatct ... tgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC

EST: gi|149076572|gb|EE165207.2|EE165207

EST:     CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAG                         ATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
genomic: CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatct ... tgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC

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), 41 (downstream exon)
Score: 26

TCCTCATGGCTTAGCTGAGGGATGGAAATGGCTCGCCATGTTCCTCAATTCTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatct ... tgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATCCTATATGTGATTTCACGGTACTTTTTACCGGCTTTGAAGGAACAAGGCA

Block sizes: 43 (upstream exon), 40 (downstream exon)
Score: 23

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 17