ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCGTGGGTTGATTGCAGAGGGTGCAGCAACTCTCCGTATGAAGCAGGATATGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgacagtgctcaactgataatctaatttcatgatatataacatcagaactaattgtttatacacatacag

Basic information

species	Zea mays
transcript	GRMZM2G032049_T01
intron #	12
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G032049_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 5'ss of exon 12

GCGTGGGTTGATTGCAGAGGGTGCAGCAACTCTCCGTATGAAGCAGGATATGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgacagtgctcaactgataatctaatttcatgatat---ataacatcagaactaattgttt-atacacatacag
 |||||||||||||| || ||||||||||| ||||| ||||| || |||||||| ||||| ||||| ||||||||||| ||||||||||||||||||||||||||  |     || || || |  | |  ||   |  |     ||||   || |||| |   | | ||   |||||||
ACGTGGGTTGATTGCTGAAGGTGCAGCAACACTCCGAATGAAACAAGATATGCAGAATGATAACAAGAATATGTCTGATTTAATAGCATATAGAATAAAAgtaagcaatgcaactgaattg-tgttttgcttgtctatttcctgataaatacacaactcacactctgatgaccatacag

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|32933496|gb|CF038308.1|CF038308

EST:     TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAA                         TTCACCCCCCATCCACATGCTGGTGACAAGTGGTGTGTCTATCCGAGCTAT
genomic: TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTAT

EST: gi|32934107|gb|CF038919.1|CF038919

EST:     TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAA                         TTCACCCCCCATCCACATGCTGGTGACAAGTGGTGTGTCTATCCGAGCTAT
genomic: TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTAT

EST: gi|32933499|gb|CF038311.1|CF038311

EST:     TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATGTAGAATAAAA                         TTCACCCCCCATCCACATGCTGGTGACAAGTGGTGTGTCTATCCGAGCTAT
genomic: TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTAT

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: 185

GCGTGGGTTGATTGCAGAGGGTGCAGCAACTCTCCGTATGAAGCAGGATATGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

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