ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaatttctggagtattgttttgagtattcagatctaaatccaaagttctgattattttttttaactgtctatag

Basic information

species	Zea mays
transcript	GRMZM5G857641_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G857641_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g63230.1 (Oryza sativa), 5'ss of exon 7

AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaatttctggagtattgttttgagtattcagatctaaatccaaagttctgattattttttttaactgtctatag
| |||||||||||||||||||| |||||||| |||||||||| |||||| ||||| || || ||||  ||||||||||| || ||||| ||||| |||||||     | ||   ||| | ||||  | | |||    | || |||   |||  |||| |    ||||||||||  | |||
AAAGTGATGTTTTTGTGTATACGTATGATGGAAATATGGCTAAAGCAGTACAGGGTCACAGAAGATTTGAAGGATTCCAAAAAACCATCAACCCAGACAGgtac---agttctaggaatgttgtaattattat----acctcaattgtaagagctgaat----tttttaactgattgtag

upper sequence: GRMZM5G857641_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA01G27000.1 (Glycine max), 5'ss of exon 6

AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggta---aatttctggagtattgttttgagtattcag------atctaaatccaaagttctgattattttttttaactgtct-atag----------
| |||||||| ||||||||||| |||||||| || ||||| |  ||||| ||||| |||||||| |  ||||| || ||||| ||||| || ||||||||||  ||    ||  |    |  | |   |  | | || |        |  | |   |||     |   ||| ||   |    ||| || |          
AAAGTGATGTCTTTGTGTATACCTATGATGGTAACATGGCCAAGGCAGTGCAGGGTCATAGGAGGTTTGAAGGGTTTCAGAAAACCATCAATCCTGACAGgttagttcacaaaatacaaatcacttcctgaattttttaatgtcatgttaagagagaaaaggggggaaattgttaagagggatctcatggtaaataatat

upper sequence: GRMZM5G857641_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G14950.1 (Glycine max), 5'ss of exon 6

AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggt--aaatttctggagtattgttttgagtattcagatctaaatccaaagttctgattatttt---ttttaactgtctatag---------------
| |||||||| ||||||||||| |||||||| || ||||| |  ||||| ||||| |||||||| |  ||||| || ||||| ||||| || ||||||||||  ||  | |  || | |      |||| | | |   | |  ||    ||||    ||   ||      | | |  ||  |||                
AAAGTGATGTCTTTGTGTATACCTATGATGGAAACATGGCCAAGGCAGTGCAGGGTCATAGGAGGTTTGAAGGGTTTCAGAAAACCATCAATCCTGACAGgttagttcacagatcagtacctgaatttttaatgtcatgctaaaagagaaaaggggggaaagttgagaactctcatggtaaataatatctgagaatctag

upper sequence: GRMZM5G857641_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT2G37980.1 (Arabidopsis thaliana), 5'ss of exon 7

AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaatttctggagtattgttttgagtattcagatctaaatccaaagttctgat-tattttttttaactgtctatag
| || ||||||||||| |||||||||||||||||||||||||  ||||| || || ||  | ||||  ||||| ||  |||| || || || || |||||||  | |    ||   | | || ||||    | |  |   | ||       | ||||| |    ||| | | || |     
AAAGCGATGTTTTTGTATATACATATGATGGGAATATGGCTAAGGCAGTACAAGGGCACCGAAGATTTGAAGGGTTTAAGAAAACTATCAATCCAGACAGgtttgaatcaatcattattcttctttttgcaact--gcctttaactttgtttactgatatgaagtttgtgaatggcag---

upper sequence: GRMZM5G857641_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT3G54100.1 (Arabidopsis thaliana), 5'ss of exon 7

AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgt-----------gggtaaatttctggagtattgttttgagtattcagat-ctaaatccaaagttctgattattttttttaactgtctatag---
| ||||||||||||||||||||||||||||| ||||||||||  || || || || || || |  |  ||||| ||   |||| ||||||| || |||||||           |  ||||  | |  | | |||    || |||  || | ||    |     || || | |||| || |   ||  |||     
AAAGTGATGTTTTTGTGTATACATATGATGGTAATATGGCTAAGGCGGTACAAGGGCACAGAAAGTTTGAAGGGTTTAGGAAGTCCATAAATCCAGACAGgtatggtaccatggaataaagcttttca-ttttggcgagattatgtagtttctttcactggttttgtgctgatttgttctgtgtgattatttcag

upper sequence: GRMZM5G857641_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv08s0007g01650.t01 (Vitis vinifera), 5'ss of exon 7

AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaatttctggagtattgttttgagtattcagatct-aaatccaaagttctgattattttttttaactgtctatag-----------------------------------
| |||||||| ||||| || |||||||| || |||||||| |  ||||| ||||| |||||||| |  ||||| ||||  ||||| || |||||||||||||  ||   ||| |    || | |||    ||||     || |||||     |  | |||     | |   ||    ||||                                   
AAAGTGATGTCTTTGTTTACACATATGACGGAAATATGGCAAAGGCAGTGCAGGGGCATAGGAGGTTTGAAGGTTTCCGAAAGACAATCAACCCTGACAGgtttgtttgtttgttttttactttttcagatattggttcctcaaatctttcttgttaattgagagtgtggccttgaaatagatggatgaatgattgttcctgttcttgtatttcag

upper sequence: GRMZM5G857641_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv13s0019g03250.t01 (Vitis vinifera), 5'ss of exon 6

AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggt----aaatttctggagtattgttttgagtattca--gatctaaatccaaagttctgattattttttttaactgtctatag
|||| ||||| ||||||||||| |||||||||||||||||||  ||||| |||||||||||| | |  ||||| || | |||||| || |||||||||| || |||    ||| |  |     ||| ||       || |   |   | | |  |   |||||    | ||||||  ||  |  ||
AGAGCGATGTCTTTGTGTATACCTATGATGGGAATATGGCTAAGGCAGTGCAGGGCCATAGGCGGTTTGAAGGGTTTCGGAAGACGATCAACCCTGACACgtaggttacaaaaatgatcagccattattccagtcctttataaaatgagaactgataatctgaca--tgtttttatatgattgcag

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|22472176|gb|BU036656.1|BU036656

EST:     CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAG                         GCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG
genomic: CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaat ... ctgtctatagGCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG

EST: gi|110198701|gb|EC880598.1|EC880598

EST:     CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAG                         GCGCAAGCTTGTCGAGTTCATTGACAAGCTAGATGAAGGTCCAATAGATTG
genomic: CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaat ... ctgtctatagGCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG

EST: gi|22818901|gb|BU498991.1|BU498991

EST:     CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAG                         GCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG
genomic: CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaat ... ctgtctatagGCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG

EST: gi|26457458|gb|CA829041.1|CA829041

EST:     CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAG                         GCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG
genomic: CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaat ... ctgtctatagGCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG

EST: gi|78544100|gb|DV621598.1|DV621598

EST:     CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAG                         GCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG
genomic: CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaat ... ctgtctatagGCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG

EST: gi|110959533|gb|EE179585.1|EE179585

EST:     CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAG                         GCGCAAGCTTGTCGAGGTCATTGACAAGCTAGATGAAGGTACAATAGATTG
genomic: CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaat ... ctgtctatagGCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG

EST: gi|50330802|gb|CO525928.1|CO525928

EST:     CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAG                         GCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG
genomic: CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaat ... ctgtctatagGCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG

EST: gi|78021117|gb|DV489504.1|DV489504

EST:     CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAG                         GCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG
genomic: CAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaat ... ctgtctatagGCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTG

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: 14 (upstream exon), 36 (downstream exon)
Score: 1

AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaat ... ctgtctatagGCGCAAGCTTGTCGAGCTCATTGACAAGCTAGATGAAGGTACAATAGATTGGACAGGGTTTGCAAGTGAGGTGAAGATGCACCATGGAAACAGGCTTGGA

Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 27

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 72

Block sizes: 35 (upstream exon), 45 (downstream exon)
Score: 17

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGTGATGTTTTTGTGTATACATATGATGGGAATATGGCTAGAGCAGTCCAGGGCCATAGGAGATACGAAGGATTCCAGAAGACCATAAACCCTGACAGgtgggtaaatttctggagtattgttttgagtattcagatctaaatccaaagttctgattattttttttaactgtctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT