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

...ttattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG

Basic information

species	Zea mays
transcript	GRMZM2G171745_T04
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g30840.2 (Oryza sativa), 3'ss of exon 7

ttattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
 | ||| | || | || |  ||      ||  ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||
-ttttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagcagGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG

upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g30840.1 (Oryza sativa), 3'ss of exon 7

--ttattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
   | ||| | || | || |  ||      ||  ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||
tgattttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG

upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 7

--------ttattatt-tttcagtgttca-----tataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
          ||| |  ||| ||| || |     | |||       ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| |||||||      
catgtgttccattctgattttagtattaaatgcttttaagtattcatatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagTTGAACAATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACC------

upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g30840.3 (Oryza sativa), 3'ss of exon 7

-----------ttattatt-tttcagtgttca-----tataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
             ||| |  ||| ||| || |     | |||       ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||         
tgtcatgtgttccattctgattttagtattaaatgcttttaagtattcatatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagAAGTTGAACAATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCG---------

upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G25690.2 (Glycine max), 3'ss of exon 7

---------------------ttattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
                     | |||||       |  |    |  ||     || ||  |  ||||   | | |||    | || |||||||  |||||||||||| ||| | ||||||||| ||||| |||||  | |||||||| ||| |   |||||||||||| ||| | ||||||| |||||| || ||   |||         
gataatataaaagtatctgactaattatacacacatagttgcctgctgttcttta-tgcttggaatatattggtcgacgtgtcttacttacttcgtggcagAAGTTACACACTGTAAGCAGGCCGACATCGACTTCAGAGGGCATGAGGAGATCTGCTCTGAATCTGGTGGAGTGATGGATTATGAAGAAGATCGAAGCCG---------

upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G25690.1 (Glycine max), 3'ss of exon 7

-ttattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
 | |||||       |  |    |  ||     || ||  |  ||||   | | |||    | || |||||||  |||||||||||| ||| | ||||||||| ||||| |||||  | |||||||| ||| |   |||||||||||| ||| | ||||||| |||||| || ||   ||||||||| ||
ctaattatacacacatagttgcctgctgttcttta-tgcttggaatatattggtcgacgtgtcttacttacttcgtggcagaagttacacactgtaagcagGCCGACATCGACTTCAGAGGGCATGAGGAGATCTGCTCTGAATCTGGTGGAGTGATGGATTATGAAGAAGATCGAAGCCGACCAAAGAG

upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 7

ttattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
||   || |       |  | | |   |    |    |  |      |||||    |   | || ||||| |  |||||||||||| ||| | ||||||||| ||||||||||| || ||||| || ||| |   ||||||| |||| ||| | ||||| |  || || || ||   |||||| || ||
ttgaaatgtgcagacatataaaaatgagttattcaaatgctgggatatgttggtcgattgtcttacttacgttgtggcagaagttacacactgtaagcagGCCGACATTGACTTCCGAGGGCACGAGGAGATCTACTCTGAACCTGGTGGAGTGATGGACTACGAGGAAGATCGAAGCCGACCCAAGAG

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|89251568|gb|DY623354.1|DY623354

EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTTTGAATCTGGAGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... atttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA

EST: gi|86472724|gb|DY239094.1|DY239094

EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... atttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA

EST: gi|32809485|gb|CD961719.1|CD961719

EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCC-AAAAATCAATCAAG                         GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... atttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA

EST: gi|50339562|gb|CO534688.1|CO534688

EST:     AGAAAGAATTTGAAGACAGAGTGGAAGAGGCCNNNNNNNTCAATCAAG                         GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA
genomic: AGAAAGAATTTGAAGACAGAGTGGAAGAGGCC-AAAAAATCAATCAAGgtgagctgga ... atttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA

EST: gi|60340320|gb|DN207293.1|DN207293

EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... atttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA

EST: gi|74242378|gb|DT650292.1|DT650292

EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... atttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA

EST: gi|78118433|gb|DV536819.1|DV536819

EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGCAG                       
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATC-A--AGgtgagctgga ... atttaagc

EST: gi|67021266|gb|CO450015.1|CO450015

EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         GCAGACATTGACTTACGGGGGCATGACGAG-CTCTCTCTGAATCTGGAGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... atttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA

EST: gi|76931005|gb|DV172591.1|DV172591

EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         GCAGACATTGACTTACGGGGGCATGACGAGTTTCTTTTTGAATCTGGAGGA
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... atttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGA

EST: gi|211192853|gb|FL432744.1|FL432744

EST:     ACCAGAAAGAATTTGAAGACAGAKTGGAAGAGGCCAAAAAATCAATCAAGCAG                       
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATC-A--AGgtgagctgga ... atttaagc

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: 47 (upstream exon), 49 (downstream exon)
Score: 97

TCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... atttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 48

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG

                                   aagttaaacaatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - ttcatat
- - - - - - - - - - - - - - - gctactg
- - - - - - - - - - - - - - - - - - - - - - - -tgttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcagaag