ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaatttcaatgtcgagagaccatttttcttttgtctggcatcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT

Basic information

species	Zea mays
transcript	GRMZM2G399073_T02
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 4

gtaatttcaatgtcgagagaccatttttcttttgtctggcatcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT
|||  || ||  |||          | | |||||| ||| ||   |||||| ||| ||  | | ||| |||||||||| | |  ||   || |||||||| |||| || |||||||| || |||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||| |||||||| || |
gtatattaaacttcgtagctgatagtcttttttgtgtggtat---atcttgttttggaaattgacttcatggcatctgctgtgggcacgtgtagATTAAGCTGGATAAGGAGAAGAAGATTCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTCATTAAGAACCTTGGGACCATTGCCAAAT

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 4

--------------------------------------gtaatttcaatgtcgagagaccatttttcttttgtctggcatcat--atcttgctttagacttgggcttgatggcatctgatatatgcttatgc---agATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT
                                       |||  |   | | |         ||||  |   |   |  | |   ||  || | |    |||   | ||    | || | | ||| |  |||   |||||||||||||||| || |||||||| ||||| ||||| || || ||||| |||||||| ||||||||| | || || ||  | || || || || || |
gttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaactaaacttaaacatgttggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 4

gtaatttcaatgtcgagagaccatttttcttttgtctggc--atcatatcttgctttagacttgggcttgatggc--atctgatatatgcttatgc---agATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT
    |   | ||   |       || || |   | | | |  | ||   |  ||  |    |   | ||     |  | || | | |||||  |||   |||||||||||||||| || |||||||| ||||| ||||| || || |||||||||||||| ||||||||| | || || ||  | || || || || ||  
-ggttagtattgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA-

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4

-----gtaatttcaatgtcgagagaccatttttcttttgtctggcatcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT
      |||| | | ||| |  | |    |||| | || ||| |  | |||  ||   | | | || |  ||  |   || ||||| |     ||||||||||| || ||||| || ||||||||||| || ||||| ||||| ||||| |||||||| ||||| ||| | || || ||| | ||||| || || || |
gttagttaatattactgttgtaaaaa---ttttgtattttcttgt-ttataatttttctgacagtttgaattcttataatatgataaa-----atgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT

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|56538364|gb|CX054073.1|CX054073

EST:     CTGATAAGAAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT

EST: gi|149004856|gb|EE039364.2|EE039364

EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT

EST: gi|24767582|gb|CA402726.1|CA402726

EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT

EST: gi|31360086|gb|CD444443.1|CD444443

EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT

EST: gi|148965480|gb|EE016290.2|EE016290

EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT

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: 154

GCATTGGATAAGATCAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 363

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

catcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT

                                  atctgat  putative branch site (score: 363)
                                     tgatatat  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttcaatgtcgagagaccatttttcttttgtctggcatcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT