ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctgaatttctattacaattcataatgtttcacgatatgaatgcatagcatggtgccacatttttgtgcaacttttttgcaagatttgcgccgtttacttgaattttattactgcag

Basic information

species	Zea mays
transcript	GRMZM2G100794_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G100794_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 5'ss of exon 4

ATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctgaatttctattacaattcataatgtttcacgatatgaatgcatagcatggtgccacatttttgtgcaacttttttgcaagatttgcgccgtttacttgaattttattactgcag
|||||| ||||||||||| ||||||||||| || ||||||||||| |||||||| ||||| ||||| ||||||||||   | ||||||||| | || | |||||||||| |||||| ||||   || |  ||   |       || |   | || || || |   ||| || |||||||| | ||||| |||||      |||| | |||||||||||  |||
ATGCAAATTTGGAGCAACATGCAAGTTTCACCACCCCCGAGAAAAAGCTGCAATTGCAACCCGAGTACAGCTGAATGCTTTAGGCTACCCATTGCGGCCGgtttgttctaaatttccattatcttttactattacttgt----tggactta-aggatagttc---attattctgcaacttctctgcaatatttgttttagttacctaaattttattaccacag

upper sequence: GRMZM2G100794_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g21700.1 (Oryza sativa), 5'ss of exon 4

ATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctgaatttctattacaattcataatgtttcacgat-atgaatgcatagcatg-gtgccacatttttgtgcaacttttttgcaagatttgcgc-cgtttacttgaattttattactgcag
 ||||||||||| ||||| |||||||||||||| ||| | || ||||||||| | ||||  || || ||| | ||||  || ||||||||  | || | |||||||||   | ||||||   |||| |   |||  |  |||     |  | ||  ||  || |   |  | |    | |||   ||||||||| ||   | || ||||| | |||||||||||||
GTGCAAGTTTGGTGCAACATGCAAGTTTCATCACCCCAGGGAGAAGGCTGCACTTGCAAACCGTGTACAGTTAAATGTTCTAGGCTACCCGATGCGTCCGgtttgttccataattctat---aattta-gttgtcacctgattgcttaatcgtaatatctgttctctacctct---tagcttgcatgcaagattagctttcattaacttgcagtttattactgcag

upper sequence: GRMZM2G100794_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 5'ss of exon 4

ATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttg-ttctgaatttctattacaattcataatgtttca--cgatatgaatgcatagcatggtgccacatttttgtgcaacttttttgcaagatttgcgccgtttacttgaattttattactgcag
 |||||||||||||| || |||||||||||||||||  |||| ||||||| ||| ||     |||||    | |||    | ||||| ||||| || | |||| | || |  |||||| ||   | ||||  |  |  |   ||| ||||||      |   ||  |   ||||      | |||   | || || |   |    | ||                 
TTGCAAGTTTGGAGCCACATGCAAGTTTCATCATCCTAGAGACAAGGCTGGAATTGCTGGAAGAGTTTCTTTAAATATTTTAGGCTATCCACTGCGGCCGgttcgattttttatttctcttt--actcatgttactggaattgatttgaatgtgcca-accatgttaggctttt------catttcccccagtttggattcaccaaatt-----------------

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|71439755|gb|DR820805.1|DR820805

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|149000507|gb|EE037687.2|EE037687

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|149083012|gb|EE172259.2|EE172259

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|71772125|gb|DR970062.1|DR970062

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|78089927|gb|DV518301.1|DV518301

EST:     AATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCCTG                         A-TGAAAAGGAATGGTGCTTATTATTTAAGAACAGGGCAGTGCAAG
genomic: AATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCC-TGgtttgttctg ... attactgcagAATGAAAAGGAATG-TGCTTATTATTTAAGAACAGGGCAGTGCAAG

EST: gi|148944209|gb|EC889301.2|EC889301

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|211078942|gb|FL257765.1|FL257765

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|211303560|gb|FL306497.1|FL306497

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|71765018|gb|DR962955.1|DR962955

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|148959485|gb|EC905484.2|EC905484

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|148946035|gb|EC891334.2|EC891334

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|78086204|gb|DV514597.1|DV514597

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGA

EST: gi|8367349|gb|BE050294.1|BE050294

EST:     CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTG                         AATGAAAAGGAATGTGCTT
genomic: CAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTT

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), 42 (downstream exon)
Score: 41

ATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctg ... attactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGAAGCACATGTAAGTTTCACCATCCACAACCATCCACTATGATGGTTGCCG

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 35

Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 33

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAACTGGGCTACCCACTCCGCCTGgtttgttctgaatttctattacaattcataatgtttcacgatatgaatgcatagcatggtgccacatttttgtgcaacttttttgcaagatttgcgccgtttacttgaattttattactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA