ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAGATACCTGAAGGTGACGTGAGATCGTTACTTTCTGACAGGGAATCGTTGGCGCCATGTGATGTAGCAGTATTTGTTTACGATAGgtacacactcctgttgagtatttatttgttcataatctgcaagtctcacaatacagtttatagtgactgactgttctccctttttgtgtatcagtcaatt...

Basic information

species	Zea mays
transcript	GRMZM2G004459_T02
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G004459_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 5'ss of exon 11

--------------GAGATACCTGAAGGTGACGTGAGATCGTTACTTTCTGACAGGGAATCGTTGGCGCCATGTGATGTAGCAGTATTTGTTTACGATAGgtacacactcctgttgagtatt-tatttgttcataatctgcaagtc-tcacaatacagtttatagtgactgactgttctccctttttg-tgtatcagtcaatt
              ||||| ||||||| ||| || ||| | |||||  |||| |||||||| ||||| || ||||||||||||||||| ||||| ||||||||   | ||      | | || ||||| || || | |   || || |||    |  || |  ||| ||||  |  | | ||| || | |||| ||       
CACTTGTATTTCGAGAGATTCCTGAAGATGATGTCAGACCATTACTGGCTGATAGGGAATCCTTGGCACCCTGTGATGTAGCAGTATTCGTTTATGATAGgtatgaattctgccaaattgttctatttatttatgaccaagaaatcctcagtgcattgtctgaagtaactggattctttacctattagctgtagcaactc---

upper sequence: GRMZM2G004459_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 5'ss of exon 12

--------------GAGATACCTGAAGGTGACGTGAGATCGTTACTTTCTGACAGGGAATCGTTGGCGCCATGTGATGTAGCAGTATTTGTTTACGATAGgtacacactcctgttgagtat----ttatttgttcataatctgcaagtctcacaa--tacagttt------atagtgactgactgttctccctttttgtgtatcagtcaatt
              || ||  |||||||||| ||  || | ||||| || || | |||||| ||||| || ||||||||||||||| ||||||| ||||||||  |  |||  |  | |||     | ||| |||||   |   |||| |    |  | || |||      || || |||||   |||| ||||||| |  ||         
CACTTGTGATGCGAGAAATTTCTGAAGGTGATGTTGGACCATTACTATCAGATAAGGAATCTTTGGCACCCTGTGATGTAGCAGTAATTGTTTATGATAGgtatgctatccactgaattatccccctctttattcatggcc-ataagttttgtcagttgcatttttctttcatggtcactga--attcttcctttttattcat---------

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|31362359|gb|CD446716.1|CD446716

EST:     TGTGATGTAGCAGTATTTGTTTACGATAG                         CTGCGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: TGTGATGTAGCAGTATTTGTTTACGATAGgtacacactc ... ctattggcagCTGCGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC

EST: gi|6637015|gb|AW261287.1|AW261287

EST:     GACAGGGAATCGTTGGCGCCATGTGATGTAGCAGTATTTGTTTACGATAG                         CTGCGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGGGAATCGTTGGCGCCATGTGATGTAGCAGTATTTGTTTACGATAGgtacacactc ... ctattggcagCTGCGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC

EST: gi|31351610|gb|CD435967.1|CD435967

EST:     GACAGGGAATCGTTGGCGCCATGTGATGTAGCAGTATTTGTTTACGATAG                         CTGCGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGGGAATCGTTGGCGCCATGTGATGTAGCAGTATTTGTTTACGATAGgtacacactc ... ctattggcagCTGCGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC

EST: gi|31352762|gb|CD437119.1|CD437119

EST:     CATGTGATGTAGCAGTATTTGTTTACGATAG                         CTGCGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: CATGTGATGTAGCAGTATTTGTTTACGATAGgtacacactc ... ctattggcagCTGCGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC

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: 45 (upstream exon), 49 (downstream exon)
Score: 160

GAGATACCTGAAGGTGACGTGAGATCGTTACTTTCTGACAGGGAATCGTTGGCGCCATGTGATGTAGCAGTATTTGTTTACGATAGgtacacactc ... ctattggcagCTGCGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCTTGCTTGATAGTTGCT

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 83

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60