ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgttctctcagctgaaagtattcatttttctgtcaattgttgttgtgctcttagtgatggcctgcctgaagcatcaggcagtgctaatatcaattatttttcttactattataagctgtgctgatgctgatgtaactcattctgaactgcatttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC

Basic information

species	Zea mays
transcript	GRMZM2G404855_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 6

--------------------------gtatgttctctcagctgaaagtattcatttttctgtca-attgttgttgtgctcttagtgatggcctgcctgaagca--tcaggcagtgctaatatcaattatttttcttactattataagctgtgctgatgctgatgtaactcattc-tgaactgcatttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC
                           | || | | |  | ||  | | || |    |   ||| | || | |  || |||  |    | ||||    | |||  | |  |  |    ||   |   | || | || || |  |   | ||     |  |||    | | |||  |||||    |   | | ||||||||||||||||||||||||||||||||| | ||||||||||| || |||||||| || ||||| ||||| ||||||||| ||||||| ||||||||| 
gtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaatgttgaagcattcttcacactggtctgatgatctctg-atcgacctgagaaatgcaaattatcctatttgtattctagccacttctattgctgtcctggacagt-taattaatgacaccattgatttgtgaacattgtccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTATGGTGATATTATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCT

upper sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 4

gtatgttctctcagctgaaagtattcatttttctgtcaattgttgttgtgctcttagtgatggcctgcctgaagcatcaggcagtgctaatatcaattatttttcttactattataagctgtgctgatgctgatgtaactcattctgaactgcatttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC
                                                      || |  |||    | ||| | || ||  |     | |   || ||     |||| ||||   |  | |  ||||  || | ||  |  |||||| ||        |  |||||||||||||||||||  ||||| |||||| |||||||||| ||||| |||||||| || ||||| || || |||||||| ||| ||||||| |||||  
-----------------------------------------------------gtaatattggtgaacttgatgtatgagaaaactgcatttggaaata-----cttagtatttggaaat-taatgatattggt-tattt--ttctgacct-------tccgcagCTTGTGAAGAATCCTGCACTTTTCGATGTACTAGTGATGCCTAACCTTTATGGTGATATTATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTT

upper sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 4

gtatgttctctcagctgaaagtattcatttttctgtcaattgttgttgtgctcttagtgatggcctgcctgaagcatcaggcagtgctaatatcaattatttttcttactattataagctgtgctgatgctgatgtaactcattctgaactgcatttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC
                                                      || |  |||      ||| | || ||  |     | |   || || ||     | ||| |  |  | |  |||  ||| | ||| |  |||||| ||        |  |||||||||||||||||||  ||||| |||||| |||||||||| ||||| |||||||| || || || || || |||||||| |||||||| || |||||| 
-----------------------------------------------------gtaatattggtgaaattgatgtatgagaaaactgcatttggaaatagtt-----agtatcaggaaat-taatgacactgct-taatt--ttctgacct-------tcctcagCTTGTGAAGAATCCTGCACTTTTCGATGTACTAGTGATGCCTAACCTTTATGGTGATATTATCAGTGACCTTTGTGCTGGCTTGATTGGAGGATTGGGCT

upper sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4

-----------------------------gtatgttctctcagctgaaagtattcatttttctgtcaattgttgttgtgctcttagtgatg--gcctgcctgaagcatcaggcagtgctaatatcaattatttttcttactatt-ataagctgtgctgatgctgatgtaactcattctgaactgcatttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC
                              | |||||       || ||   |  || |   ||| ||||    | ||  |     | ||   |      |  |   | ||      |    | | ||  ||     | || ||    |  | | || |||      |     |||   ||    | || |   ||||||||||| || || |  ||||||||||| || ||||||||||| |||||||| || || || |||||| | ||||||||  |  |||||||  | || |
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaatt-ctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC

upper sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 4

gtatgttctctcagctgaaagtattcatttttctgtcaattgttgttgtgctc----ttagtgatggcctgcctgaagcatcaggcagtgctaatatcaatt---atttttcttactattataagctgtgctgatgc-tgatgtaactcattc-tgaactgcatttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC
||| | | |  || | |||  || | ||||||  || ||||    | ||| ||     | | |||  |||    ||   |  ||   |   |  || ||| |   ||||   ||    || |   ||||  | |    ||   ||    | |  | | ||  |  | ||| ||||||||||| || || |  ||||||||||| || |||||||||||||| || |||||||| ||||||||||| ||||| || ||| |||| ||  | ||  
gtaagctatgaca-ccgaatctact-attttttcgttaattaagttagtggtcgggactcgggatcaccttgtagatttagaagtttggtttcttagcaacttgtatttgagttctgcttttccactgtttttacatgtggaatatgcgactgataatcttgagatacctgcagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAACCTGTACGGTGACATTATTAGCGATCTGTGTGCCGGATTGGTTGGAGGACTAGGAT

upper sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 4

gtatgttctctcagctgaaagtattcatttttctgtcaattgttgttgtgctcttagtgatggcctgcctgaagcatcaggcagtgctaatatcaattatttttcttactattataagctgtgctgatgctgatgtaactcattctgaactgcattt---gcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC
                                                                       ||  ||     |      | |||| |         |  ||    ||        |||     |   |  || ||| |  |   | |        |||||||||||||||||||  ||||||||||| || |||||||| ||||||||||||||||| ||||| ||||| |||||||| |||||||||||  | ||| 
--------------------------------------------------------------------gcaaaatatgtaagaaaaacgagatcattctaggcatatgatacagaaatgcactaggataaaactaggaaccactctaacttctctcttgaataaacagCTTGTGAAGAATCCTGCGCTTTTTGATGTGTTGGTGATGCCTAACCTCTATGGTGACATTATTAGTGATCTCTGTGCTGGCTTGATTGGGGGACTAGGCT

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|14204192|gb|BG837869.1|BG837869

EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

EST: gi|60355306|gb|DN222279.1|DN222279

EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

EST: gi|6166676|gb|AW144940.1|AW144940

EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

EST: gi|60354405|gb|DN221378.1|DN221378

EST:     ACCCTGAAATTCAATACGAGGAGGTCATTATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

EST: gi|6952333|gb|AW424401.1|AW424401

EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

EST: gi|6195048|gb|AW147152.1|AW147152

EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAA
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAA

EST: gi|148958341|gb|EC904565.2|EC904565

EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

EST: gi|60350137|gb|DN217110.1|DN217110

EST:     ACCCTGAAATTCAATACGAGGAGGTCATTATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

EST: gi|33102686|gb|CF062646.1|CF062646

EST:     ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: ACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

EST: gi|71310901|gb|DR791753.1|DR791753

EST:     AGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: AGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

EST: gi|76908322|gb|DV162882.1|DV162882

EST:     AGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT
genomic: AGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTAT

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: 103

TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctc ... ttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 229

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 161

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 272

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attataagctgtgctgatgctgatgtaactcattctgaactgcatttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC