ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag

Basic information

species	Zea mays
transcript	GRMZM5G804382_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccatt--ctattgactgataatatgagactagcgataagctaatt-cataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag
 || |||||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| || |||||||| || |||||||| ||||| || || |||||||| || || |||||    |  |  || ||  | || |   |    | |||   |   ||   |   ||   |||    ||| |||  | ||||  |||                           
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgtttgatttaagcccataaatttctatcttatttt-tgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctc-ttctagttat--------------------------

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattc-tattgactgataatatgagactagcgataagctaatt-cataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag
 || |||||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| || |||||||| || |||||||| ||||| || || ||||||   || || |||||   | |  | |     | || |   |    | |||   |   ||   |   ||   |||    ||| |||  | ||||  |||                           
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctc-ttctagttat--------------------------

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 25

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtct-acttggcattgcattctgattagcaaatccatccattcatgtaacacag
 ||||| ||||| ||  | |||||||| |||||||| || ||||| |||||||||||||||||||| || ||||| |||||||| || ||||| |||||||| |  ||    |  ||||  ||   ||| ||||  | |||  |    |   |  ||  ||   | |     |||  |||| |   |     ||       ||||                     
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCGGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttga-aataccaaact--cttctattcatatctcaaaaccttgccaggtcccactttgtggtttgacctctgctaaaaatt--------------------

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtct-acttggcattgcattctgattagcaaatccatccattcatgtaacacag
 ||||| ||||| ||  | |||||||| |||||||| || ||||| |||||||||||||||||||| |||||||| |||||||| || ||||| |||||||| |  ||    |  ||||  ||   ||| ||||| | |||  |    |   |  ||  ||   | |     |||  |||  ||| |     ||      |||||                     
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttga-aatatcaaact--cttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt--------------------

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcg-ataagctaattcataaggtcctagtctg--tctacttggcat--tgcattctgattagcaaatccatccattcatg-taacacag--------------------------------------------------------------------
 ||||||||||| ||  | |||||||| |||||||| |||||||| |||||||||||||||||||| || || || |||||||| || ||||| |||||||  || ||     |   ||  ||  || |  || | | |||   | ||  |  ||||    |    ||||  |    |   |||||||  |||| | |||    |   | ||   |   ||| |    | |                                                                    
GTCAAAGAAAGACAATCTTTACAAGGACTGTATGGAAACATGCTCTCAATCTGGTGACCGTGAACTCTCGGAAGATTTGCTTGTCTACTTTATTGAGCAGg--tgtttattttcttgtccttttccttaagatctcaaactctggtattcgtaaattagatactaactaggttagacccttttggcatagtgcactttgacc--ctgcttcacttagaaatgattttgctgctttctttcctcacctcccgcaccagtttttctctcttaattaacaaagggattatattgatttgcag

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcg-ataagctaattc-ataaggtcctagtctgtctacttggcattgcattctgat--tagcaaatccatccattcatgtaacacag-----------------------------------------------------------------
 ||||||||||| ||  | |||||||| |||||||| |||||||| |||||||||||||||||||| ||||| || |||||| | || ||||| |||||||  || ||     |   ||  ||  || |  |||| | |||   | ||  |  ||||  |||    |   ||  | |   ||||||| |     |||   |     |   |   |||  | |    |                                                                   
GTCAAAGAAAGACAATCTTTACAAGGACTGTATGGAAACATGCTCTCAATCTGGTGACCGTGAACTTTCAGAAGATTTGCTTATCTACTTTATTGAGCAGg--tgtttattttcttgtccttttccttaagatatcaaactccagtattcgtaaattagatactaactaggttagaccttttggcatagtgcagtgaccctgcttcacttagaaattattttgctgctttctttcttcacctccagtgctggttcttttcttttaattaacaaagggattatattgatttgcag

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 26

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag
 ||||||||||||||| | ||||| |||   |||||||||  ||||||||||||||||||||||||  | ||||| |||||||| ||||| || || |||||       ||  | |||  |  | |  |||||     | |    |  | | | | |  |   | ||  | |  |   ||    ||| |  || |   || || | |                  
GTCAAAGAAAGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgt---accaaattcaatttcaacggcatataattc---attttttagcaac-attgcccagcattctcatttaacatgttttatttgaagactaagatgctaagcta------------------

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 26

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag-
 |||||||| |||||| | ||||| |||   |||||||||  ||| ||||||||||||||||||||  | ||||| |||||||| ||||| || || |||||   |   ||  | |||  | || |  |||||                   | ||  ||    | | | |   |      |||||    | ||  | |   |  ||| |  |||| |||||    
-TCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCGCAATCTGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGGt---gccaaattcaatttcaatggcatataat-----------------tcattttttagcaacattgcccagcagaccagcattatgatttgggttg---actcattc--tcatttaacatttt

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattcta---ttgactgataatatgaga-ctagcgataagctaattcataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag
 |||||||| |||||| | ||||| |||   |||||||||  |||||||||||| || ||||||||  | ||||| |||||||| ||||| || || |||||   | | ||  |  ||  |   || |   |||||       || || |||   |  || || ||||  ||   |   |  | |  | ||  || || |||                           
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgt---gctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtt-taccattattcttggataatgtgttttgtttaat-------------------------

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaaccca-------ttctattgactgataatatgagactagcgataagctaattcataaggtcc--tagtctgtctacttggcattgcat-tctgattagcaaatccatccattcatgtaacacag---------
 |||||||||||||||||||||||||| |||||||| ||    || ||||| || |||| ||| ||  ||||  |  | || || || || || || ||||| ||| |      ||       ||  || ||  |  | ||    | |  | |     ||    ||| |||     ||   | ||| |||| | || |  |   |||  ||   || |   |  ||||    | |         
GTCAAAGAAAGATAACATGTACAAGGACTGTATGGAAACTGCTTCGCAATCCGGCGACCATGATCTTGCAGAACAACTTCTCGTCTACTTCATTGAACAGgtatggataggtttcaggcaggattacatcgaaagccattagtctattttcaactttttaccgtatatggtaaaacagaaagacta-ttggtactgaagatgaaatttacatccccgttgttgtatgttgtgctggttttacag

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccat--tctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag
|||||||||||| |||||||||||||| |||||||| ||    |||||||| || || | ||||||  ||||  |  | || |||||||| || || ||||| || |        |   | ||     || || |   || |   |  |  | | | |   || |   | |||       |   | | | || | |             ||   |  ||| | ||||
ATCAAAGAAAGACAACATGTACAAGGACTGTATGGAAACGGCTTCACAATCAGGCGAACATGAACTTGCAGAACAACTACTGGTGTATTTCATTGAACAGgtatgatgatggttaaacatttacgagatgctagtgctagccattcagtttggttagttgaaaagaattggtccagacgttgaacgtagtatcccg-----------tgtcttctgctgttatacag

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtctacttggcattgcattctgatta-gcaaatccatccattcatgtaacacag
 || |||||||| ||| ||||||| ||    ||||||||   ||| ||||||||||||||||||||  ||||||| |||||||| ||||| || ||| ||||         |||||   |  |       ||| |||    | |  |    ||| |   || | | |||||| || ||     ||   ||    || |  ||  | ||| || |    ||||    
GTCGAAGAAAGACAACCTGTACAAAGACGCGATGGAGACTGCCTCGCAATCTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAGgt---------acccagaatgctag--agcaatctgaagacatctct---ttaact---aaagccatagtct-tccac--aatataaaat--caatcacacaccttcatgcactagcataac----

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 27

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag
 ||||||||||| ||| | ||||| |||   |||||||||||||| || ||||| || ||||||||  ||||||| |||||||| ||||| || |||||||| ||  | | |  || |    || ||   ||      | | | ||||| |    |||| |  | |||    || |   ||    | |||    |||  | |||   |                 
GTCAAAGAAAGACAACCTATACAAAGATGCGATGGAGACATGCTCTCAGTCTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtcatatacact----tgtctataaaagctgaaattgagataatc---atcatcaaatgctaaatagtgtgaatgttccttcat--aaattttctaattttta----------------

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|33093317|gb|CF053311.1|CF053311

EST:     CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttga ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC

EST: gi|32945927|gb|CF050746.1|CF050746

EST:     GACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: GACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttga ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC

EST: gi|24934286|gb|CA452504.1|CA452504

EST:     CTGGTGTTCGTGAAGTGTCATAGGACTTGCTTGTGTATTTTATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttga ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC

EST: gi|89761296|gb|DY689368.1|DY689368

EST:     CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttga ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC

EST: gi|32846264|gb|CD985945.1|CD985945

EST:     CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttga ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC

EST: gi|32847239|gb|CD986920.1|CD986920

EST:     CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttga ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC

EST: gi|71765800|gb|DR963737.1|DR963737

EST:     CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttga ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC

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: 237

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttga ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACT

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

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 226

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG