ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CCAGTACGTCTCCAAGCGCTGGCCCTACTGGAACAGGACGGAGGGGGCCGACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacggacgctaccgatgcagctaggaatgcagagcatggagttccagcctagccatttcccccatacacagcgagcttgcactcagagttgatatatatgcttgctgctgtccag

Basic information

species	Zea mays
transcript	GRMZM2G059845_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G059845_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g10080.1 (Oryza sativa), 5'ss of exon 2

CCAGTACGTCTCCAAGCGCTGGCCCTACTGGAACAGGACGGAGGGGGCCGACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacggacgctaccgatgcagctaggaatgcagagcatggagttccagcctagccatttcccccatacacagcgagcttgcactcagagttgatatatatgcttgctgctgtccag
| ||| | ||||||||  |||||||||||||||||| |||||||| || || |||||||||||    ||||||||||||| ||||||||||||||||||||||||| | | ||           || |  | || | ||  ||    || |||  ||    |   | ||||  | |   |  |   | | ||| |  | |  |  | ||  ||  |     
CAAGTTCATCTCCAAGTACTGGCCCTACTGGAACAGAACGGAGGGTGCGGATCATTTCTTCGTTGTGCCACATGACTTTGCAGCGTGCTTCTACTTCCAGgtgagtcatgtaca----------aggttcggattcggaaaat----tttcag--taattttgaactccattgagaagaaatt---atttagactgcaaactttagttttttgtggatt--

upper sequence: GRMZM2G059845_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G37920.1 (Glycine max), 5'ss of exon 2

CCAGTACGTCTCCAAGCGCTGGCCCTACTGGAACAGGACGGAGGGGGCCGACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacggacgctaccgatgcagctagga-atgcagagcatgg--agttccagc-------ctagccatttcccccatacacagcgagcttgcactcagagttgatat----atatgcttgctgctgtccag--------------------------------
 |||    | ||      |||||| || ||||||||||| || ||||| || |||||||| || || || ||||||||||| || |||||| | |  || || ||  |   |   ||||| |  |  |  |  ||    | ||     ||||| |         | | | | ||      |     | |||   |  ||  || || ||      |||||      | | |                                    
ACAGCTTATTTCTTCAAACTGGCCTTATTGGAACAGGACAGAAGGGGCAGATCATTTCTTTGTGACCCCTCATGACTTTGGGGCATGCTTCCATTATCAAgtaagaaatttagtgtaccgttttaattttgctattttcatcactattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccag

upper sequence: GRMZM2G059845_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G17140.1 (Glycine max), 5'ss of exon 2

CCAGTACGTCTCCAAGCGCTGGCCCTACTGGAACAGGACGGAGGGGGCCGACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacggacgctaccgatgcagctagga-atgcagagcatgg--agttcc-------agcctagccatttcccccatac------acagcgagcttgcactc-agagtt---gatatatatgcttgctgctgtccag--------------------------
 |||    | ||      |||||| || ||||||||||| || ||||| || |||||||| || || || ||||||||||| || |||||| | |  || || ||  |   |   ||||  |  |  |  |  ||  | | ||     |||||        |  | | | | ||      |        |||  || | || | || |   ||   ||| || |||  |  ||                                  
ACAGCTTATTTCTTCAAACTGGCCTTATTGGAACAGGACAGAAGGGGCAGATCATTTCTTTGTGACCCCTCATGACTTTGGGGCATGCTTCCATTATCAAgtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccag

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|91876290|gb|EB406247.1|EB406247

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|91876209|gb|EB406166.1|EB406166

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|211437112|gb|FL416893.1|FL416893

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAATGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|88756465|gb|DY540606.1|DY540606

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|76011529|gb|DT938699.1|DT938699

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|211215552|gb|FL199927.1|FL199927

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         TAAGAGAAG-CCATCCAGCGAGGTGTCCT
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCT

EST: gi|149099210|gb|EE185237.2|EE185237

EST:     AACATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|78114761|gb|DV533149.1|DV533149

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|71434936|gb|DR815986.1|DR815986

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|94479511|gb|EB708469.1|EB708469

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|78074303|gb|DV502737.1|DV502737

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|148944961|gb|EC890130.2|EC890130

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|71432339|gb|DR813389.1|DR813389

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|93284342|gb|EB676606.1|EB676606

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACG

EST: gi|71313729|gb|DR793454.1|DR793454

EST:     ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAG                         GAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTA
genomic: ACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTA

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), 33 (downstream exon)
Score: 24

CCAGTACGTCTCCAAGCGCTGGCCCTACTGGAACAGGACGGAGGGGGCCGACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacg ... tgctgtccagGAAGAGAAGGCCATCCAGCGAGGTGTCCTCCCGGTGCTGCGCCGCGCTACGCTGGTCCAGACGTTTGGGCAGAAGAACCATGTCTGCCTCAGGGAAGGCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGTACGTCTCCAAGCGCTGGCCCTACTGGAACAGGACGGAGGGGGCCGACCATTTCTTCGTCACTCCACATGACTTTGGAGCGTGCTTCTACTTCCAGgtgagtgacggacgctaccgatgcagctaggaatgcagagcatggagttccagcctagccatttcccccatacacagcgagcttgcactcagagttgatatatatgcttgctgctgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG