ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtaatcttcaacccaactttgtaaaaaatcatatcatgcacctttttttacaatttactgagctcattctattctattctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG

Basic information

species	Zea mays
transcript	GRMZM2G152686_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 5

gtaatcttcaaccca-actttgtaaaaaatcatatcatgcacctttttttacaatttactgagctcattctattct-attctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG
|||||  | | |||  || || | |||| |   |||  |||| | ||        ||| | ||    || | || | ||||||||| | |||||| || |||||||| || ||||| || ||||||||||| ||||| || ||| |||| ||||||||||||||||| ||||||
gtaataattatcccctacattatgaaaatt---atccagcacttattcaactgtcttaat-agtgtgttttgttttgattctcagGCTCCAATGCCGATATACATGTAATTGTAAAGATTGAAAGTGCAGATTCCATTCCAAACCTACACTCAATCATCACAGCATCGGATGGG

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 5

------------------------gtaatcttcaacccaactttgtaaaaaatcatatcatgcacctttttttacaatttactgagctcattctattctattct-cagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG
                         || | || ||   |  | |   |  | |  |       |  |   ||   ||| |  | |  |  ||| | |  || || |||| |||  |||||| |||||||| ||||||||||| |||||||||||||| || || || || |||||||| ||||| ||||||||||||
gtaaatatctaaaatattttaaaaatactttttaaa--atttatccgattagttttgctgcatatttagattataaatatgataaatt--ttccacttgatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCATCTGATGGG

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 5

gtaa-tcttcaacccaact-------ttgtaaaaaatcatatcatgcacctttttttacaatttactgagctcat------tctattctattct-cagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG
|||| | |||||   |  |       || |||  | ||         |  || | | |  ||||    |  | ||      || | || |  || |||| ||  ||||||| ||||| || || |||||||| |||||||||||||| || || ||||| |||||||| || ||||| |||||||||
gtaaatattcaagatacttgtattttttttaattagtccatctgattaatttctctaattatttcaaaatgtgataaattgtccactcaacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 5

------------------------gtaatcttcaacccaactttgtaaaaaatcatatcatgcacctttttttacaatttactgagctcattctattctattct-cagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG
                         || | || |||   | ||    ||  |   |       |  ||  ||   ||| |  | |  |  ||| |||   | || |||| ||   |||||| |||||||| ||||||||||| |||||||||||||| || || || || |||||||| ||||| || |||||||||
gtaaatatctaaaatattttaaaaatactttttaac---atttatccaattagtttgctgcatatattgattataaatatgataaatt--ttccatttggtactgcagGCTGTGGTGCTGATATACATGTCATCGTAAAAATCGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCGTCTGATGGG

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 5

gtaa-tcttcaa------cccaactttgtaaa--aaatcatatcatgcaccttt-------ttttacaatttactgagctcattctattctattct-cagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG
|||| | |||||         || ||| | ||  |  || | | ||  |  | |       ||||| | | |  | |  |   || | || |  || |||| ||  ||||||| |||||||| || |||||||| |||||||||||||| || || ||||| |||||||| || ||||| |||||||||
gtaaattttcaagatacttgtaatttttttaattagttcgtctgattaatttctctaattattttaaagtatgataaatt--gtccactcaacactgcagGCTGTGATGCTGATATACATGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 5

--------gtaatcttcaacccaacttt-gtaaaaaatcatatcatgcacctttttttacaattta---ctgagctcattctattc---tattctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG
         |       |  ||| | |  || ||  ||      |||    ||  |||    | ||    |||| |  ||   | |   ||||  ||| | |   |||||| ||||| || || || ||||| || |||||||||||||| || ||||| || || || ||||||||||| ||||||
gtaaatacttggaacctattccatcctaagtgaatgatttgcctatgatatttcctttttggtctaaccttgagattgtttgttacaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5

-------------gtaatc--ttcaacccaactttgtaaaaaatcatatcatgcacctttttttacaatttactgagctcattct--attctattct--cagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG
              || ||  ||  |   ||||   |||        ||| || |  ||  || | | |||||       | |||  |   | ||    |||| || ||||| || || ||||| || || ||||| |||||||| |||||||| |||||  |||||||||| || || ||||||||||||
gtaaatacttaggatattcatttggaaataactaaataacttgcttgatc-tgtaatttgcttcaaattttaccacttataatctttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG

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|108954033|gb|EC364981.1|EC364981

EST:     TTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGATTATCTAAAAA                         GTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGNCTCCA
genomic: CTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGATTATCTAAAAAgtaatcttca ... ctattctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCA

EST: gi|14204276|gb|BG837953.1|BG837953

EST:     TTATCTAAAAA                         GTTGCAATGCTGACATACATKTTATCGTAAAAATARAAAGTGCAGACTCCA
genomic: TTATCTAAAAAgtaatcttca ... ctattctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCA

EST: gi|211141481|gb|FL154590.1|FL154590

EST:     TTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGATTATCTAAAAA                         GTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCA
genomic: CTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGATTATCTAAAAAgtaatcttca ... ctattctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCA

EST: gi|67025561|gb|CO454310.1|CO454310

EST:     TTTTGTGAAGGATGCTCAAGTTGTCCACGAACTCAAGGATTATCTAAAAA                         GTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCA
genomic: CTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGATTATCTAAAAAgtaatcttca ... ctattctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCA

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: 316

GACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGATTATCTAAAAAgtaatcttca ... ctattctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 233

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 504

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcatatcatgcacctttttttacaatttactgagctcattctattctattctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG