ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGTGGGGCTTTTACATGGAAGAGACCGAGAAGAATTACGCTGAGGATACCAAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATGgtcagttcacttcagcgtcatgccatgtgatggtggttattccttctggttcgaagacgcggatgttcttaacttttttttttttacattcacccggaaatttgttgcag

Basic information

species	Zea mays
transcript	GRMZM2G024576_T01
intron #	18
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G024576_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os05g02670.1 (Oryza sativa), 5'ss of exon 19

AGTGGGGCTTTTACATGGAAGAGACCGAGAAGAATTACGCTGAGGATACCAAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATGgtcagttcacttcagcgtcatgccatgtgatgg-tggttattccttctggttcgaagacgcggatgttcttaacttttttttttttacattcacccggaaatttgttgcag
|||||||||||||||||||||| || ||||||||||||  ||| |||||||  ||||| ||||| |||||||| ||| |||| ||||||||||| ||||||| ||| | |   | | |     ||||   ||  | || || ||||||| |  |   |  ||||    |  |  | |   | ||| ||  |  |    |  |    |||||
AGTGGGGCTTTTACATGGAAGAAACTGAGAAGAATTACATTGAAGATACCACTGCAGTGGACAGTGGAAGGTCGTGCTTGGCAGAAGTGCTTGTGGAATGgtgagtactcagtatcatggcatcatgctgtgaattgtgataccttctgctatgct-atacggaatcacggatgtctcaatgtttgaccattgct---atctcaactgcag

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|148955137|gb|EC900654.2|EC900654

EST:     AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATG                         CAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC
genomic: AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATGgtcagttcac ... tttgttgcagCAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC

EST: gi|148945804|gb|EC891090.2|EC891090

EST:     AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATG                         CAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC
genomic: AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATGgtcagttcac ... tttgttgcagCAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC

EST: gi|26457141|gb|CA828724.1|CA828724

EST:     AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATG                         CAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC
genomic: AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATGgtcagttcac ... tttgttgcagCAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC

EST: gi|20811178|gb|BQ295656.1|BQ295656

EST:     AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATG                         CAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC
genomic: AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATGgtcagttcac ... tttgttgcagCAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC

EST: gi|101382782|gb|EB813446.1|EB813446

EST:     AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATG                         CAAGGCGAAAGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC
genomic: AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATGgtcagttcac ... tttgttgcagCAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC

EST: gi|101382780|gb|EB813445.1|EB813445

EST:     AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATG                         CAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC
genomic: AAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATGgtcagttcac ... tttgttgcagCAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTC

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: 208

AGTGGGGCTTTTACATGGAAGAGACCGAGAAGAATTACGCTGAGGATACCAAAGCAGTCGACAGCGGAAGGTCTTGCCTGGCCGAAGTGCTTGTAGAATGgtcagttcac ... tttgttgcagCAAGGCGAAGGCCACCGTGGGTGCACAGCAATGGAAGAACGCGGAGGATTCTCTGTTCAGCCTCGGCAAAGGAAACGTGGAGTCAGTGGATTCTATAGTC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 39

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 23