ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtacattacatcatgtcatgaagtccacacaaagtatgcaatcaatcagtctcagtccacataaagtatgcaatcaatcattctcccacagtagttcttgaagaactcacttgatgtcctcatctttttttttctaacag

Basic information

species	Zea mays
transcript	GRMZM2G443985_T04
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G443985_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 5'ss of exon 5

CACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtacattacatcatgtcatgaagtccacacaaagtatgcaatcaatcagtctcagtccacataaagtatgcaatcaatcattctcccacagtagttcttgaagaactcacttgatgtcctcatctttttttttctaacag
||| ||||||||| ||||||||||||| || ||||| ||||||||||||||||||||||||| |||||||||||||||||  | | ||||||| ||||||| ||    |||| ||     |||  ||||||| | | ||||||||  | ||||     | | |     |  | || ||   |   |  |||   ||||    |                                          
CACATGTGGAGGACTGTGCCCTGGACTGAACACTGTCATTAGGGAAATTGTATGTGGCTTATATGACATGTATGGTGTCAGTAGGGTACTTGGAATTCAGgcaagt--cattgcactgcatcacaaagtccatatacagtatgcaggcgatca----tatttccttctagttctgaaaattactttattcctgaagtatcattcat---------------------------------------

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|211132978|gb|FL170883.1|FL170883

EST:     TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAACACCATCACCTTGACTCCAAAG
genomic: TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG

EST: gi|148972520|gb|EE023481.2|EE023481

EST:     TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
genomic: TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG

EST: gi|13557855|gb|BG549211.1|BG549211

EST:     TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTTTTATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
genomic: TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG

EST: gi|76921243|gb|DV168509.1|DV168509

EST:     CACCAAGATACTTGGGATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
genomic: CACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG

EST: gi|211132969|gb|FL170874.1|FL170874

EST:     TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAACACCATCACCTTGACTCCAAAG
genomic: TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG

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), 47 (downstream exon)
Score: 81

CACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAGAGTGTAAATGACATTCACAAAAGGGGTGGAACTATTCTTGGATCATCTC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 88

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118