ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttctcaactattccttccagtagattgctacagtacatgtctgatcattttatatttgtgctcttgtcatcgttgcaactgtataaaatggtg...

Basic information

species	Zea mays
transcript	GRMZM5G807639_T03
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G807639_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 9

GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttctcaac-tattccttccagtagattgctacagtacat-gtctgatcattttatatttgtgctcttgtcatcgttgcaactgtataaaatggtg
||||| ||||||||||||||||||||||||||||||||| | |||||||| || ||||| |||||||||||  | ||||||||||||||||||||||||||   |   |  |  |   ||   ||| ||  |      |||   |  |   | |    |||    |  || |||  | ||  ||   |   ||    
GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaacatgatgtcatttatcttttagttttttctttatcatcacccaaatgtatatggttttaaatggtgacatt-tggcccctaattttgattta-

upper sequence: GRMZM5G807639_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv10s0116g01480.t01 (Vitis vinifera), 5'ss of exon 12

GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttctcaactattccttccagtagattg-ctacagtacatgtctgatcattttatatttgtgctcttgtcatcgttgcaactg--tataaaatggtg--
|| || ||| ||||  | ||||| ||| ||||||  ||| | || |||||||| ||||| |||||||||||  | ||||| ||||||||||| ||||||||  | |    ||    ||  | ||  |||  || |||   | |    |||||||   ||||| | |||    | | |||   |   | ||     |||  
GTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagt--tgtatgttacagtttgaattattttgattatagtcagtattatctcatttt---tttgtccacttaatgtagctgcctttcattttagccaagtgcc

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|67025111|gb|CO453860.1|CO453860

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|32935625|gb|CF040437.1|CF040437

EST:     ATTCTCAGAACACCTTTGCAATGCTGA-GTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ATTCTCAGAACACCTTTGCAATGCT-ATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|7031253|gb|AW461141.1|AW461141

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|60343714|gb|DN210687.1|DN210687

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|31349005|gb|CD433362.1|CD433362

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|6056485|gb|AW090875.1|AW090875

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAG-TGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|211169877|gb|FL077606.1|FL077606

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACRNKTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|6020821|gb|AW065749.1|AW065749

EST:     GATTCTCAG-ACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|67031724|gb|CO460473.1|CO460473

EST:     GATTCTCAGAACACCCTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGGC-CAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

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: 115

GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225