ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaagccaaaggcacaccatgcgtattttagactcaaattttgcactgactgatttcactttgttgtcag

Basic information

species	Zea mays
transcript	GRMZM2G051004_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 5'ss of exon 10

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaagccaaaggcacaccatgcgtattttagactcaaattttgcactgactgatttcactttgttgtcag
||||||||||||| || ||||| ||||||||||| |||||||||||||| ||||||||||  |||||||||||||||||||||||||||||||| ||||||     | |||||     ||| ||| | || |||| |    |||||  ||||||| ||| | |   || | ||
CCACCCAGAAGACTGTCGATGGCCCTTCAATGAAAGATTGGAGAGGAGGGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAGgtacgatgaaccaaaaatctaccttgctt-ttctagatttctgttttg-gctgactgttttgattcc-ttattag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA16G09020.1 (Glycine max), 5'ss of exon 10

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctga-agccaaaggcacaccatgcgtattttagactcaaattttgcact---gactgatttcactttgttg--tcag--
| || || ||||| || ||||||||||| |||||||||||| |||||||| | || || |  ||||| |||||||| || || |||||||| || ||||||   ||  |    |  || |   |  |  || ||   |||    | | | |   || |   ||   ||| |    |||   
CAACACAAAAGACTGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAGgtacaagatggatggacacagattttatgctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G22790.1 (Glycine max), 5'ss of exon 10

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctga-agccaaaggcacaccatgcgtattttagactcaaattttgcact---gactgatttcactttgttg--tcag--
| || || |||||||| ||||||||||| |||||||||||| |||||||| | || || |  ||||| |||||||| || || |||||||| || ||||||   ||  |    |  || |   |  |  |  ||   |||    | | |     || ||  ||   ||| |    |||   
CAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAGgtacaagatggatggacacagattttatgcttactattttcagtgctggtatatgagattgggtttgttttataaaatcacag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G16300.1 (Arabidopsis thaliana), 5'ss of exon 10

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaagcc--aaaggcacac-catgcgtat--tttagactcaaatttt-gcactgactgatttcactttgttgtcag
| || ||||| || || || || || ||||||||||| ||||||||||| || || ||  | |||||||| ||||||||||| || || || ||||||||| |  ||     | ||  | |   |  | ||   | | || ||| ||||  ||  |||||  |||   | | |    ||
CTACTCAGAAAACTGTGGACGGCCCATCAATGAAGGACTGGAGAGGAGGCCGAGGCGCAAGTCAAAACATCATTCCTAGCTCAACAGGCGCTGCAAAGgtacccaaatttgtacagttatatataaacatagcatctggaatcatatttaagccatgacttttttacttgtctcaatag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G79530.1 (Arabidopsis thaliana), 5'ss of exon 10

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgta-gctgaagc---caaaggcacaccatgcgtattttagactcaaattttgcac--tgactga--tttcactttgttgtcag----
| || ||||| || |||||||| || ||||||||||| ||||||||||| || || ||| | |||||||| ||||||||||| || || || || ||||||  |  || |   ||  |  |   || || | |  |   |  ||||   | |   |  ||||  | |   ||| |  |||     
CTACTCAGAAAACTGTTGATGGGCCATCAATGAAGGACTGGAGAGGAGGTCGGGGCGCTAGTCAAAACATCATTCCTAGCTCAACCGGCGCCGCGAAGgtacacaaaaactcacatggttatcgcaagcatgtaattatcctaaatcgggaatcatatctgagctgtggttttttgatcaagtag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 5'ss of exon 10

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaag--ccaaaggcacaccatgcgtattttagactcaaattttgcactgactgatttcactttgttgtcag-----
|||| ||||||||||| ||||| |||||||||||||||||| |||| || || ||||||   ||||| || || || |||||||||||||| |||||||||   || |     ||  ||||      |||   |    | || || | ||  |  ||||||    |  |||  |      
CCACACAGAAGACCGTGGATGGGCCTTCAATGAAGGATTGGCGAGGGGGCCGAGGTGCTTCACAAAATATCATCCCAAGCTCCACTGGTGCTGCAAAGgtatgagatggatttaattcacat-ggaagtagaatcccataaagttgtacaaggtgtgattttgactgtttggtatcatag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S309_84V6.1 (Physcomitrella patens), 5'ss of exon 8

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaagccaaaggcacaccatgcgtattttagactca-aattttgcactgactgatttca-ctttgttgtcag-------------------------------------------------------
||||||||||||| || || || || ||    ||||| ||| | ||||||||||||||||| || ||||| ||||||||||| ||||| || |||||||||       | | ||    | | |  |    |   |||||  |   |||  | | | || | | |    ||||| |                                                       
CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATCATTCCTAGCTCAACTGGAGCTGCAAAGgtactgtgcacgacagttgaatccttggcgagt-gcactcatgaggctgctgtaagttatgtgagcggaattgtctgcactgattcaacattggcctgatcgtcgctttcctcgttcgggattttcaaacag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S309_73V6.3 (Physcomitrella patens), 5'ss of exon 7

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaagccaa-aggcacaccatgcgtattttagactcaaattttgcactgactgatttcactttgttgtcag---------------------------------------------------
| |||||||||||||| || ||||| ||    ||||| ||| | ||||||||||||||||| || ||||| ||||| ||||| ||||| || || |||||| |||    ||  |     ||| || ||  || |||    | |  || |     ||| |  | ||   ||| |                                                    
CTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATTATTCCCAGCTCAACTGGAGCTGCGAAGgta-ctgtgctcattatttggaccctg-gtggtt-agatgggactgctgtaagttgtgaatggagttgtctgtaaagtctgaacataggcctgatcccaattttcgtgactcgggattttcatgcag

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|37397668|gb|CF636141.1|CF636141

EST:     GACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAG                         GCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC
genomic: GACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaag ... ttgttgtcagGCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC

EST: gi|67025324|gb|CO454073.1|CO454073

EST:     GACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAG                         GCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC
genomic: GACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaag ... ttgttgtcagGCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC

EST: gi|40337147|gb|CK371217.1|CK371217

EST:     GACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAG                         GCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC
genomic: GACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaag ... ttgttgtcagGCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC

EST: gi|84977532|gb|DW475954.1|DW475954

EST:     GACGTGGTGCTGGCCAAAACATGATTCCTAGCTCCACTGGTGCAGCAAAG                         GCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC
genomic: GACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaag ... ttgttgtcagGCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC

EST: gi|148944446|gb|EC889561.2|EC889561

EST:     AAACATAATTCCTAGCTCCACTGGTGCAGCAAAG                         GCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC
genomic: AAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaag ... ttgttgtcagGCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCC

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), 39 (downstream exon)
Score: 158

CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaag ... ttgttgtcagGCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGACTTGACATGCCGGA

Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 34

Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 38

Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 245

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGgtagctgaagccaaaggcacaccatgcgtattttagactcaaattttgcactgactgatttcactttgttgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG