ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaatggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgtttcag

Basic information

species	Zea mays
transcript	GRMZM2G136803_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 20

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttcccatcca--ttacagtgttgcattaagataatt--tgggaatataatgaaaagagcgttctgattgaaaatggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgttt-cag
|||||||||||||| || |||||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||| || | |   ||||   | | || || | | |||  |    ||  |   | |     ||| |   ||  ||    |    | ||  |||| ||| |   | ||||||       |||| |  |  | ||| |||
GTTATGCAAGAACTTGGATTGATTGGATTGCGTATCCAGAGAATGCCCAGTGAACCAAACTTGGAATTTGGTATTCCATCTCAGTATAGCTACATGACGgtgcgtttcccttctgtttacttgggttcaatatgttcattgctacagatgcacacatacttaggttgtatatggcaaactaaaaatggtttggagaagctattcagtttgatgttcaattttgtgtcatatttttttcag

upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA19G30580.1 (Glycine max), 5'ss of exon 21

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaatggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgtttcag
||||||||||||||||| ||  |||| ||||| || ||  | ||||| | ||||||  |  |||||||||||||||||||| |||| ||||| ||||||||  | |    | |  |    | |||| |        |||    || | ||  |     ||||  | |||||      | ||| |   |  ||   | | |   || ||                           
GTTATGCAAGAACTGGGATTAGTTGGGTTGCGCATTCAGCGCATGCCCAATGAACCTGATCTGGAATTTGGTATTCCTTCTAAGTACAGCTACATGACGgtaaggt----ttctatgttctattgcttctcctccttttccttattttatttaggtgccgtt--ggttgaact---aatggaaacatattgactttttatatttttat---------------------------

upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G27600.1 (Glycine max), 5'ss of exon 20

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcg-ttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaatggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgtttcag
||||||||||||||||| ||  |||| ||||| || ||  | ||||| | ||||||  |  |||||||||||||||||||| |||| ||||| ||||||||  | || | ||    ||  |  |  | ||    | ||||     |||   |        | | | | | |      ||    ||||        |||| || |||||                            
GTTATGCAAGAACTGGGATTAGTTGGGTTGCGCATTCAGCGCATGCCCAATGAACCTGATCTGGAATTTGGTATTCCTTCTAAGTACAGCTACATGACGgtaaggtttcaatgtgctattgcttgtccttttccttattt-----tatttaggtgttgttggtttaactaatggaaacatattgatttttt----ctgtttttattga----------------------------

upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv08s0040g00670.t01 (Vitis vinifera), 5'ss of exon 19

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaatggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgtttcag
|| |||||||||||||| || ||||| || || || ||||| ||||| ||||||||     |||| ||||||||||||||||| |||||||||||||||||  | ||| ||      || | ||||  ||    | ||| ||  | |  |   | |     |    ||| |  |  |  | |  |  |  ||  |  | ||||||  |                           
GTCATGCAAGAACTGGGTTTAATTGGTTTACGCATTCAAAGGATGCCAAGTGAACCTGGGCTGGAGTTTGGTATTCCTTCTCAATATAGCTATATGACGgtaagatcctat-----gcaatattgctctact-catttttggcctgttctattaggg----tgcatttggatgtcccgtgaaagtggaaggatcccat-ttgattagtag-------------------------

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|32932784|gb|CF037596.1|CF037596

EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA

EST: gi|32930716|gb|CF035528.1|CF035528

EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTTTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA

EST: gi|32931864|gb|CF036676.1|CF036676

EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTTTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA

EST: gi|16927586|gb|BM080655.1|BM080655

EST:     TGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: TGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA

EST: gi|32867796|gb|CF007478.1|CF007478

EST:     AACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: AACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA

EST: gi|32932809|gb|CF037621.1|CF037621

EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA

EST: gi|32837361|gb|CD977039.1|CD977039

EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA

EST: gi|32836690|gb|CD976368.1|CD976368

EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGC
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGC

EST: gi|32932023|gb|CF036835.1|CF036835

EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGC-CTTACATTACGTGCTTGGTGGGA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCT-ACATTACGTGCTTGGTGGGA

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: 46 (upstream exon), 48 (downstream exon)
Score: 42

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 36