ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTATGGGTAATCATGTTGGTGTTACAATTGGTGGTGCCAATGGGCATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGAgtatgctttctactatcatacttcaatacggttaatttactatagggactctttctagcctcataaccctcttgttgatttaggtacataatgttaatatatgagttggtaactttaacctcgtgatttttactgcaaatgtcttataacctttccctttttcaacag

Basic information

species	Zea mays
transcript	GRMZM2G010823_T01
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 13

GTTATGGGTAATCATGTTGGTGTTACAATTGGTGGTGCCAATGGGCATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGAgtatg--ctttctactat-catacttcaatacggtta-----atttactatagggactctttc---tagcctcataa-ccctcttg----ttgatttaggtacataa---tgttaatatatgagt-----tggtaactttaacctcgtgatttttactgcaaa------tgtcttataaccttt--ccctttttcaacag
||||||||||||||||||||||| ||| | |||||| | ||||| ||||||||  ||||||| |||||||||||||| ||||| ||||||||| |||||||  || |||| ||| ||| | |||||| | | |     ||    || |     |  ||     | |  ||||| ||||| ||    |  ||   | ||||      || |||||  |   |     || | |||||         | | ||  ||   |      ||  | ||   || |  | ||| ||| ||||
GTTATGGGTAATCATGTTGGTGTCACAGTAGGTGGTTCGAATGGACATTTTGAGTTGAATGTCTTTAAGCCAATGATTGCAGCTGGATTACTTAGAgtatgatctctctattatacatgcctcaatatgctaatatgtatcctttacaaaattttctttaaacaactacataaaccctcatgcatctgtatcctgttacactgagttgctaatacctctatacctctgcttactttctttctaatactgttcgtgggcaccagtttgagtgatgttctatacctcttcttctacag

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|60342181|gb|DN209154.1|DN209154

EST:     ATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGA                         TCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC
genomic: ATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGAgtatgctttc ... ttttcaacagTCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC

EST: gi|60357469|gb|DN224442.1|DN224442

EST:     ATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGA                         TCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC
genomic: ATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGAgtatgctttc ... ttttcaacagTCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC

EST: gi|149089383|gb|EE178622.2|EE178622

EST:     CAGCCGGATTACTTCGA                         TCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC
genomic: CAGCCGGATTACTTCGAgtatgctttc ... ttttcaacagTCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC

EST: gi|6022572|gb|AW067384.1|AW067384

EST:     ATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGA                         TCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC
genomic: ATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGAgtatgctttc ... ttttcaacagTCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC

EST: gi|5901092|gb|AW042192.1|AW042192

EST:     ATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGA                         TCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC
genomic: ATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGAgtatgctttc ... ttttcaacagTCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTC

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: 231

GTTATGGGTAATCATGTTGGTGTTACAATTGGTGGTGCCAATGGGCATTTTGAACTGAATGTTTTTAAGCCAATGATCGCAGCCGGATTACTTCGAgtatgctttc ... ttttcaacagTCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361