ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTCAACACCTGTGCTCCTTGTTCTTCCTGTAGTGACCTTCTATTTCCACAAGTACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAGgtatgtttccttctaaaatctgggaggtgaataaatgtgtgacctaaatacagttagatcattaaaaaccatgtttaaaacggtcgcaccatggagcatgactaccaacacatttccatttcgttaccag

Basic information

species	Zea mays
transcript	GRMZM2G021194_T01
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G021194_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g35050.4 (Oryza sativa), 5'ss of exon 11

GTCAACACCTGTGCTCCTTGTTCTTCCTGTAGTGACCTTCTATTTCCACAAGTACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAGgtatgtttccttctaaaatctgggaggtgaataaatgtgtgacctaaatacagttagatcattaaaaaccatgtttaaaacggtcgcaccatggagcatgactaccaacacatttccatttcgttaccag
||||||||| |||||||||||||| ||||| || ||||| |||||| | || |||||||| || |||||  | ||  |||||||| |||  ||||| ||||||    || |   | |||| |           | | |||    ||| |    ||     ||||||    |  ||   ||       || ||     |   ||                           
GTCAACACCGGTGCTCCTTGTTCTCCCTGTTGTAACCTTTTATTTCTATAAATACTGCAAGAATCGCTATGAGCCTGCTTTTGTGGAATATCCATTACAGgtaatgctcatctcagaatcagtttatcatgccactatgtattttaagtt---tttatctattaaaccttagcttgtgaaataaaaaacaatattaaaattct---------------------------

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|32843604|gb|CD983285.1|CD983285

EST:     ACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: ACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|4624416|gb|AI615249.1|AI615249

EST:     TTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: TTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|32831867|gb|CD971545.1|CD971545

EST:     ACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: ACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|60351312|gb|DN218285.1|DN218285

EST:     AGTACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

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: 47 (upstream exon), 47 (downstream exon)
Score: 86

GTCAACACCTGTGCTCCTTGTTCTTCCTGTAGTGACCTTCTATTTCCACAAGTACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGACCTCAAAGGATACCTAATGAATGCCTACATCCACCCGGTGTTCAAAGGTG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 132

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207