ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgacaatagtttcagtttcaaagttctgaagtacttactgagtggaccctgcagtgtgatggtgaactaattgttatgctggtaatcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA

Basic information

species	Zea mays
transcript	GRMZM2G092719_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g08440.1 (Oryza sativa), 3'ss of exon 2

gtgacaatagtttcagtttcaaagttctgaagtacttactgagtggaccctgcagtgtgatggtgaactaat--tgttatgctggtaatcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA
|||| |||  |  |  | |||  ||  ||      ||  ||| | |    | ||||   || ||  ||| ||  |||||| |||      || |||||||||||||||||||||||||||| |||||||| |||||||||||||||||||| || || || |||||||| ||||||||||||||||| || |||||||
gtgaaaatgatcaccatgtcacggtagtgcg----ttggtgaattggg--tacagt---attgtttactgatcgtgttatcctgaattatgtctgcagCCAATCAAGGAGTCTGCTCTGGGAAACATCCCGACCATTGCCTTCTGTGACACCGATTCCCCAATGCGGTATGTCGATATCGGCATCCCGGCCAACAACA

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G17000.1 (Glycine max), 3'ss of exon 2

-----------------------------------------------------------------------------------gtgacaat--agtttcagtttcaaagttctgaagtacttactgagtggaccctgcagtgtg-atggtgaactaattg---ttatgctggtaatcgtt-tgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA
                                                                                    ||    |  ||  |  |||| ||| ||||||   | | |||||        |   |||    |  ||   | |||    ||||| |  | ||  || ||||||| ||||||||   |||||| || || || ||||| ||||| || ||||||||||| ||||| |||||||| || ||| |||| ||||| || || || |
gttattacccctttagaagttataaccagagagtattaaaggtgttttcaggagttatattgttcaacttttaaccgtcaaggatgtttgttgagggttggtttgaaatttctga--cagtaactgatcttgtttttttgtgcctgtcctgccatgatttgccttatgttattgatttttgtgcagCCTATCAAGGAAGGTGCTCTTGGAAATATTCCAACTATTGCTTTTTGTGACACTGATTCTCCAATGCGGTATGTTGATGTCGGGATCCCTGCCAATAATA

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 2

gtgacaatagtttcagtttcaaagttctgaagtacttactgagtggaccctgcagtgtgatggtgaactaattgttatgctggtaatcgtttgc-agCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA
       ||  || | | |     | |   |  | ||  ||| |  ||  || ||  |  ||||      | ||   |  ||||    |||||| |||||||||||||   |||| |||| ||||| ||||| ||||||||||||||||| || ||||| ||| | |  ||||| || || || || || |||||||
------gtatattgaatgt-gttttacctcatcagttg-tgatttaactgtgtaggtttttggttttgctaatgcggttttggtttgtgtttgccagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G72370.2 (Arabidopsis thaliana), 3'ss of exon 2

gtgacaatagtttcagtttcaaagttctgaagtacttactgagtggaccctgcagtgtgatggtgaactaattgttatgctggtaatcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA
       ||   ||   |||| |    | |  |||| | ||| ||     ||   | || |  |||  ||| |||  ||   ||      |||||||| ||||||||   |||| |||| ||||| |||| |||||| ||||||||||| |||||||| ||| | |  || || || || |||||||| |||||||
------gtaaactc---ttcatatgattcatatact-agtgattgattaatgatttttgttattga--taaatgtcttgtgtgtg-----ttgcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGACACAGACTCTCCAATGAGATTTGTTGACATTGGTATCCCAGCCAACAACA

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 2

gtgacaatagtttcagttt--caaag--ttctgaagtacttactgagtggaccctgcagtgtgatggtgaactaattgttatgc-tggtaatcgtttgca--gCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA
  || ||| |     |  |  |||||  || ||  |   |||  |  || |  ||| | ||   |  ||||     || | ||  ||||  ||| ||| |  |||||||| |||| |||||||||| ||||| ||   ||| || ||||||||||| |||||||| |||  |||||| || || |  ||||| ||||||||||
--gagaatggccaaggaatggcaaaggattttgtggagattaaagtatgcagactgta-tgaatttctgaaacgggtggtttgtgtggtgttcgattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGACACGGACTCTCCGATGAAGTACGTGGACATTGCTATCCCTGCGAACAACA

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|29544407|gb|CB604787.1|CB604787

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|149000198|gb|EE037342.2|EE037342

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|30306899|gb|CD001572.1|CD001572

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|28361631|gb|CB239987.1|CB239987

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAAACATCCCAACCATTGCCTTCTGTGA
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAA-CATCCCAACCATTGCCTTCTGTGA

EST: gi|148982964|gb|EE028852.2|EE028852

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|28931357|gb|CB334718.1|CB334718

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|8367495|gb|BE050440.1|BE050440

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGTTCTGGGGAACCATCCCGACCATTGCCTTTTGTGA
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAA-CATCCCAACCATTGCCTTCTGTGA

EST: gi|4681187|gb|AI629857.1|AI629857

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCT
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCT

EST: gi|31910443|gb|CD651426.1|CD651426

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGC

EST: gi|28361815|gb|CB240171.1|CB240171

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|30087521|gb|CB885727.1|CB885727

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|18659186|gb|BM500199.1|BM500199

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCGACCATTGCCTTTTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|50330906|gb|CO526032.1|CO526032

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|32940408|gb|CF045227.1|CF045227

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCGACCATTGCCTTTTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|30705679|gb|CD058872.1|CD058872

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGAC

EST: gi|29544542|gb|CB604922.1|CB604922

EST:     TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAG                         CCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGA
genomic: TCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGA

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: 315

CGCTGGGAGGCACACCCCTGGTACATTCACTAATCAGCTCCAGACCTCCTTCAGCGAGCCTCGACTGCTCATCCTTACTGACCCAAGGACTGACCATCAGgtgacaatag ... tcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 363

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agtggaccctgcagtgtgatggtgaactaattgttatgctggtaatcgtttgcagCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA