ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgaccttccttgcaaattggatatacatttcaacacgttcaagcataaatctgcctacttccccatctaattgtgtttctccttttgtgaaccag

Basic information

species	Zea mays
transcript	GRMZM2G120115_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5

AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgaccttccttg------caaattggat---atacatttcaacacgttcaagcataaatctgcctacttcccc----------atctaattgtgtttctccttttgtgaaccag
|||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||| |||||||||  |||||| ||||||||       | |       | || ||||    | |  ||  | ||||| |||||  |  ||||  |  |  |           |||| ||||||| ||||||  | |    |||
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcag

upper sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G01960.1 (Glycine max), 5'ss of exon 5

AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacctt----ccttgcaaattgg------atatacatttcaacacgttcaagcataaatctgcctacttccccatctaattgtgtttctccttttgtgaaccag---------
|| || || || || ||||| || ||    || ||   |||||||||||| || |||||||||||||||||||| |||||||| |||||||||||||| ||||  | |  ||    |||  ||  || |      | | |||||     || |  |    ||||| |    ||||     | ||||| |     |   | |   |              
AGAGAGCAAGGCATTCAAGAAATCCAGTCGCAGATTGGTGAAGTAAATGAGATTTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCAATGATTGgtaacttagtttttcccctcccagttttgctaattacacacattcttgtac-tatatttttaaatgtctagacttttttttttaattttaaactttgatgtaaaatttccattttgtag

upper sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5

AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgta----------------tgtgaccttccttgcaaattggatatacatttcaacacgttcaagcataaatctg--cctacttcc-ccatctaattgtgtt---tctccttttgtgaaccag
||||| || || || ||||| || ||||| |||||   |||||| ||||| ||||||||||||||||||||||| |||||||| |||||||| ||||| ||||                | ||  ||||||    | ||| || |  |||| |     |  |   ||   ||||  |||  |  | | |||||||     |   | || ||||||       
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctttattttactgaatgaatttatttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag-----

upper sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G13410.1 (Glycine max), 5'ss of exon 5

AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc----ttccttgcaaattggatatacatttcaacacgttcaagcataaatctgcctacttccccatctaattgtgtttctccttttgtgaaccag
||||| || || || ||||| || || || |||||   |||||| ||||| |||||||||||||||||||| || |||||||| |||||||| ||||| ||||  | |      | ||||      |   |    | ||  |    |       |  | ||||  || |  ||   |     |   | || ||||||       
AGGGAGCAAGGCATTCAAGAAATACAGCAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTACTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccattcccttttgttcttcctggttacttgtatctttattttactgtacctgctcacattacctagtgccactaaatttcattttgtag-----

upper sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G33950.1 (Glycine max), 5'ss of exon 5

AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgaccttccttgcaaattggatatac-atttcaacacgttcaagcataaatctgcctacttccccatctaattgtgtttctccttttgtgaaccag------------------
|| ||||| || || ||||| |||||    |||||   |||||||||||| || |||||||||||||||||||| |||||||| |||||||||||||| ||||  | |   |  |  |    ||  | | | | ||  |||| ||| ||    || ||   |  ||     ||||    ||||| |  || | |||   |                   
AGAGATCAAGGTATTCAAGAAATTCAGTCGCAAATTGGTGAAGTAAATGAGATTTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCAATGATTGgtaacttagtgttttcccttcatgcttttgctaattacacacattctagttctaa-ctctatttttaaatgtctagacttgtttttttttatttgatgtaaaatatttccattttgtag

upper sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5

AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgaccttccttgcaaattggatatacatttcaacacgttcaagcataaatctgcctacttccccatctaattgtgtttctccttttgtgaaccag
||||| |||||||||||||| || || ||||||||    || || ||||| || |||||||||||||||||||| |||||||| |||||||  ||||| ||||  | | ||  ||  |   |      | |  |  |   | ||   |  | |  ||||  |||  | ||| | |     |||||| |||          
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgtctagagttcgct--attccctttctgattcaggctgctgact--ctcatttca----atttctcttttcag-------

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|71444906|gb|DR825956.1|DR825956

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|71310156|gb|DR791369.1|DR791369

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|211365944|gb|FL391110.1|FL391110

EST:     CCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: CCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|33770632|gb|CF272926.1|CF272926

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|76290013|gb|DV029581.1|DV029581

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|60394595|gb|DN227465.1|DN227465

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|78108843|gb|DV527260.1|DV527260

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|18660756|gb|BM501031.1|BM501031

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAAT-CTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|37392993|gb|CF633751.1|CF633751

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCAACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|88749057|gb|DY533198.1|DY533198

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|84977510|gb|DW475932.1|DW475932

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|6952519|gb|AW424587.1|AW424587

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGCAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

EST: gi|50328759|gb|CO523885.1|CO523885

EST:     AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTA

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: 48 (upstream exon), 48 (downstream exon)
Score: 138

AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgacc ... tgtgaaccagATGACATTGATTCCCATATAGAGAATGCTGTTGTAGCGACTTCGCAGGCTAAAGGTCAGCTTTCAAAAGCTGCCAAGACTCAGAAGTCGAACTCTTCGCT

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

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtatgtgaccttccttgcaaattggatatacatttcaacacgttcaagcataaatctgcctacttccccatctaattgtgtttctccttttgtgaaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA