ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaatcatttgtagcttgttccttatcatttgaggggatgacgaaattgatccttgtttcagataaactatagaaaaatgtcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG

Basic information

species	Zea mays
transcript	GRMZM2G078756_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4

gtaaatcatttgtagcttgttc----cttatcatttgaggggatgacgaaattgatccttgtttcagataaactatagaaaaatgtcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG
|||||  | || ||| | ||||     || |||    ||    | |  ||||  ||   ||  |  | | || |||| | |||  |  | |||||||||||| || ||||||||||||||||||||||||||||| || ||||| |||||||| ||||| ||||||||||||
gtaaactagttatagttagttctgtctttgtcaccaaagaaatttatcaaat--atatatgcattggtttaaatataaagaaacat-gtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 6

---gtaaatcatttgtagcttgttccttatcatttgaggggatgacgaaatt--gatccttgtttcagataaactatagaaaaatgtcatc----tgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG-----------------------
    |    ||| |    ||        || || | |  |  |  |    ||   ||     | || |   |  |||||          |     | |||||||||| || ||||| ||||| || || || ||||||||||| || ||||| ||||| || |||||||||||  ||                       
agcctcctccatctccctctaaccaaacattatgtaaatgattttctttttttaaatagccttctctgcgcatttatagtttttcccttttgcgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCGTTTGAACTTGAAATATATTTCAAGGCATGCTATGCATACTTATCTCT

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4

------------------------------------------gtaaatcattt-----gtagcttgttccttatcatttgaggggatgacgaaattgatccttgtt----tcagataaac---tatagaaaaatgtcatctg-------------------cagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG
                                          |||||| | ||      | | || ||     |  |||  |  ||| |    ||| ||    |      |  |  |||     ||  || ||| | |||||                   ||||| | || |||||| |||||||||| ||||| |||||||||||||| ||||| |||||||| || ||||||||| ||
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 4

--gtaaatcatttgtagcttgt--------tccttatcatttgaggggatgacgaaattgatccttgtttcagataaactatagaaaaatgtcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG------------
   | ||   | || |   | |        |  || |||| |  |||  |  |  |     |      |     |   ||| |      ||  || |||||||  ||| || ||||| ||| |||| ||||| ||||| || ||||||||||| ||||| || || ||||||||||||            
tcttgaaatttctgaaatctatcagaaaggtagttttcatcttggggtttaccatatactgtatagaatctgtgtgggcta-aatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 4

--gtaaatcatttgtagcttgttcc--------ttatcatttgaggggatgacgaaattgatccttgtttcagataaactatagaaaaatgtcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG
   ||||   | || |   | |           || |||| |   ||  |  |  |     |      |     |   ||| |      ||  || |||||||| ||| || ||||| ||| |||| ||||| ||||| || ||||||||||| ||||| || || ||||||||||||
ccttaaaatttctgaaatctatcagaaaggaggttgtcatcttgaggtttaccatatactgtatggaatctccgtgggcta-aatctgttgaaatttgcagGTGATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ35873 (Selaginella moellendorffii), 3'ss of exon 4

gtaaatcatttgtagcttgttccttatcatttgaggggat-gacgaaat--tgatccttgtttcagataaactatagaaaaatgtcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG
                       | | | || |   |  | || |||||  |||    ||  |||       |||     ||||      |||||    ||||||||||||||| | ||||| ||||||||||| ||||| || || |||||||| |||||||  ||  ||
----------------------gtaagctttggtaagcctcgatgaaatcatgacttgtgcatcaatctgtttatgctgtaatg------gcagGGAACGTAGAGATGCGATGGATAGACACGTACTTCCCATTCACCAATCCGTCTTTTGAGCTGGAAATATTCTTCAAG

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|31072245|gb|BQ479053.1|BQ479053

EST:     AGCTGCAGAACTCAAGAAAACACTGGAAGGATTGGCAAGACATCTATTTG                         GTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCAT
genomic: AGCTGCAGAACTCAAGAAAACACTGGAAGGATTGGCAAGACATCTATTTGgtaaatcatt ... tcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCAT

EST: gi|71762613|gb|DR960550.1|DR960550

EST:     AGCTGCAGAACTCAAGAAAACACTGGAAGGATTGGCAAGACATCTATTTG                         GTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCAT
genomic: AGCTGCAGAACTCAAGAAAACACTGGAAGGATTGGCAAGACATCTATTTGgtaaatcatt ... tcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCAT

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: 47

TTCTCTCCTGATGAATGGTCAGGTTCTGGCTTGGATGGGACAGCATATGCAGCTGCAGAACTCAAGAAAACACTGGAAGGATTGGCAAGACATCTATTTGgtaaatcatt ... tcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 80

Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 49

Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 46

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ggatgacgaaattgatccttgtttcagataaactatagaaaaatgtcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG