ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattttatgcgcatgtgctactggtttgaaacttggagaatcacagtttctgattacaatataacaagttgttcaaatgcag

Basic information

species	Zea mays
transcript	GRMZM2G002807_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 5'ss of exon 5

TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattttatgcgcatgtgctactggtttgaaa---------cttggagaat----cacagtttctgattacaatat----aacaagttgttcaaatgcag--------------------------------------------------------------
||| || ||| |||||||||| ||||| ||||||||||||||||| || || |||||||||||| | ||||||||| ||||| |||| |    | ||| | ||  ||||||||| |||  |         ||||   | |    ||   | |  |  |  || ||    ||       || | |||||                                                               
TGCGGAGCAATTGGTGGACATTGGCTGCCAATGGGTTATTCTTGGGCATTCAGAGCGTAGACATGTCATTGGTGAAGATGATCAGgtaagcgctatatacacagatgctactggattggtagttctctcacttgtccacttgtccatgctgttagcctgtaacattctgaaggcacctttgagatgcatgattgctgttgacatgcagtagttctgattgggattgtgacataccatgtttataaatgcag

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G20930.1 (Glycine max), 5'ss of exon 5

TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattttatgcgcatgtgctactggtttgaaact-tggagaatcacagtttct----gattacaat--ataacaagttgttcaaatgcag--------------
||  || |||||    ||| | |||||  | ||||||||||||||||| |||||||| |||||| | ||||| ||||||||||||||||  |||||      |  | |||  |   |    || ||||  |  |   ||| |    ||| | |||  |||| || |     ||    ||              
TGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAGgtgaaaattttggagataatttctatagtagttttcctatggaccagtattatttgtaaaagatgaaaatgtataataattataataaccaaagattgcaaactccag

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G06740.1 (Glycine max), 5'ss of exon 5

TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattttatgcgcatgtgctactggtttgaaacttggagaatcacagtttctg------attacaat--ataacaagttgttcaaatgcag----------
||  || |||||    ||| | |||||  | ||||||||||||||||| |||||||| |||||| | ||||| ||||||||||||||||  |||||      |  | ||| | ||      | | | ||     | | | ||      || | |||  |||| |   |   | ||    |          
TGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAGgtgaaaattttggagataccttcta-tagtagttttcctagggaccagtattctttgtaaaagatgaaaatgtataatatactaaccgaagattgcaaactccag

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G36990.2 (Glycine max), 5'ss of exon 5

TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtga--ttattttatgcg-catgtgctactggtttgaaacttggagaatcacagtt--tctgattacaata--taacaagttgttcaaatgcag---------------------
 || ||||||||    ||  | || ||  | |||||| |||||||||| |||||||| |||||||||||||| |||||||||||||| |    | |  |  |  ||| |       ||        | |||||| |   ||  | |  || ||| |  |   || |  || | ||                         
CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaatccagacatcatttttctacagtagctttgctagagaat-atgattagtatatttgcaagagatgctaaatatttaagatattaactgaacattgtcaattccag

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G34300.1 (Glycine max), 5'ss of exon 5

TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtga--ttattttatg---cgcatgtgctactggtttgaaactt----ggagaatcacagtt--tctgattacaatata----acaagttgttcaaatgcag----------------------
 || ||||||||    ||  | || ||  | |||||| |||||||||| |||||||| |||||| ||||||| |||||||||||||| |    | || |     |   | | |    | ||||   |||     |||||| |   ||  | |  || ||| | |     |||  | || ||   |                        
CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaattcagaaatcatttctacagtagctttgctgctttgctagagaat-atgattaatatatttgcaagagatgatgcaaaatatttaagatcttacttgaatattgtcaactccag

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 5'ss of exon 5

TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgatta--ttttatgcgcatgtgctactggtt---tgaaacttggag----aatcacagtttctgattacaatataac--aagttgt--tcaaatgcag----------------------
||  |||||| ||   || || |||||  | |||||||| ||||| ||||||||| | |||||| ||||||||||| ||||| ||||||  |  | | ||       || ||||  ||   |||||| || ||    | ||| |  || |  ||     ||||   ||| | |  ||| |    |                      
TGTGGAACAATTGAAAGATATTGGCTGCAACTGGGTTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaactctaatattagattgttactatttatgtgaaacgtgaagctatattcagaactttttttttttggataagtgaagctatattcagaacttgactgtgggtctgaaattttcag

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|31910617|gb|CD651514.1|CD651514

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAA
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAA

EST: gi|211221682|gb|FL287478.1|FL287478

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGC
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGC

EST: gi|211221686|gb|FL287482.1|FL287482

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGGTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|71315805|gb|DR794555.1|DR794555

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGT-ATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|28910278|gb|CB331359.1|CB331359

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATC
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|211221681|gb|FL287477.1|FL287477

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|211221688|gb|FL287484.1|FL287484

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAA
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAA

EST: gi|31406430|gb|CD485162.1|CD485162

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAG
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAG

EST: gi|71432050|gb|DR813100.1|DR813100

EST:     TTATTCTTCGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|148967122|gb|EE018295.2|EE018295

EST:     AATTCTTTGGACACTCTGAGCGTAAACATATTATTGGTGAAAATGAGGAG                         TTTATTGAAAAGAAGGCTGCATATGCATTGA
genomic: TATTCTT-GGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGA

EST: gi|31405819|gb|CD484551.1|CD484551

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|74237679|gb|DT645593.1|DT645593

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|211221680|gb|FL287476.1|FL287476

EST:     TATTCTTGGACACTCTGAGCGTAGGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAAT
genomic: TATTCTTGGACACTCTGAGCGTAG-ACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAAT

EST: gi|74234869|gb|DT642783.1|DT642783

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|76283252|gb|DV022820.1|DV022820

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAGGGCTGCATATGCATTGAGCCAAAATGTAAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|21760201|gb|BQ635742.1|BQ635742

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|19821928|gb|BQ047952.1|BQ047952

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGTCTGCATATGCATTGAGCCAAAAT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAAT

EST: gi|5268718|gb|AI770682.1|AI770682

EST:     TTATTCTTGGACACTCTGAGCGTANACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|74244594|gb|DT652508.1|DT652508

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

EST: gi|211221679|gb|FL287475.1|FL287475

EST:     TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG                         TTTATTGGAAAGAANGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

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: 116

TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgattattt ... tcaaatgcagTTTATTGGAAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108