ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GCCCCACATGTTTATCAATGGGTACAAGAACGTGCTTGCTGTTGCTGTGGAGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtgtttcattgtgccatgtcaattatttcgagcaatttaagtccatgtataaatctacttcatttaatcaccatgcttatcttcgaatttgtc...

Basic information

species	Zea mays
transcript	GRMZM2G179976_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G179976_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g03640.1 (Oryza sativa), 5'ss of exon 4

GCCCCACATGTTTATCAATGGGTACAAGAACGTGCTTGCTGTTGCTGTGGAGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgta-----gtgtgtgtttcattgtgccatgtcaattatttcgagcaatttaagtccatgtataaatctacttcatttaatcaccatgcttatcttcgaatttgtc
 || ||||||||  |||||||||||||||| ||||||||||||||||||||||| || |||||||||||||| || || ||||||||||||||  | || |||     || | | ||||| | |   |||    ||  ||   ||    ||| |      |  ||  || |  ||  |      ||    ||  |  |||     
ACCACACATGTTCCTCAATGGGTACAAGAATGTGCTTGCTGTTGCTGTGGAGACCGAATACTCGTACCCACATGCTGATAAGATCAAGGAGTATTTGAAAgtaatcttgtttctatttcactttatgatgatgttttcttaatgcttgataattggtctaactaagataatcaatagatagtagattaccatactaaaat-----

upper sequence: GRMZM2G179976_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g03880.1 (Oryza sativa), 5'ss of exon 4

GCCCCACATGTTTATCAATGGGTACAAGAACGTGCTTGCTGTTGCTGTGGAGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtgtttcattgtgccatgtcaattatttcgagcaatttaagtccatgtataaatctacttcatttaatcaccatgcttatcttcgaatttgtc--
||| ||||||||  |||||||||||||||| ||||| ||||||||||||||||| || ||||| |||||||| || |||||||||||||||||  | ||||||   |   ||  |||     || ||  ||  || ||    |  | |   | | ||      |  |  | | || |  |   |    | | ||  |||   
GCCACACATGTTCCTCAATGGGTACAAGAATGTGCTCGCTGTTGCTGTGGAGACCGAATACTCATACCCACATGCTGACAAGATCAAGGAGTATTTGAAGgtaacctagtttctatttcataatttccctt--tttgatgtctaaatgcgtaagaattgtctgaggtagtctgataattagattgcggtactaagctgtagc

upper sequence: GRMZM2G179976_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g04070.1 (Oryza sativa), 5'ss of exon 4

GCCCCACATGTTTATCAATGGGTACAAGAACGTGCTTGCTGTTGCTGTGGAGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtgtttcattgtgccatgtcaattatttcgagcaatttaagtccatgtataaatctacttcatttaatcaccatgcttatcttcgaatttgtc--
||| ||||||||  |||||||||||||||| ||||||||||||||||||||||| || ||||| |||||||| || || ||||||||||||||  | ||||||   |   ||  |||     || ||  ||  || ||    |  | |   | | ||      |  |  | | || |  |   |    | | ||  |||   
GCCACACATGTTCCTCAATGGGTACAAGAATGTGCTTGCTGTTGCTGTGGAGACCGAATACTCATACCCACATGCTGATAAGATCAAGGAGTATTTGAAGgtaacctagtttctatttcataatttccctt--tttgatgtctaaatgcgtaagaattgtctaaggtagtctgataattagattgcggtactaagctgtagc

upper sequence: GRMZM2G179976_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ38349 (Selaginella moellendorffii), 5'ss of exon 4

GCCCCACATGTTTATCAATGGGTACAAGAACGTGCTTGCTGTTGCTGTGGAGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtgtttcattgtgccatgtcaattatttcgagcaatttaagtccatgtataaatctacttcatttaatcaccatgcttatcttcgaatttgtc
  | |||   ||  ||||    ||||||||||| |||||||| ||| ||| |||||| |||||||| ||||| ||||| |    ||||||||| ||||||||  ||    |||| ||||  |||    |   | || | || | |   ||     |    || |                                    
AACGCACTACTTCCTCAACTCTTACAAGAACGTTCTTGCTGTCGCTCTGGCGACTGATTACTCGTATCCACATGCCGAGACTGCCAAGGAGTATCTCAAGgtt-tgatcttttccttgt--catcagcagggtctctaacattctc--tcttccaacttttccag-----------------------------------

upper sequence: GRMZM2G179976_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ14871 (Selaginella moellendorffii), 5'ss of exon 4

GCCCCACATGTTTATCAATGGGTACAAGAACGTGCTTGCTGTTGCTGTGGAGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtgtttcattgtgccatgtcaattatttcgagcaatttaagtccatgtataaatctacttcatttaatcaccatgcttatcttcgaatttgtc
  | |||   ||  ||||    ||||||||||| |||||||||||| ||| |||||| |||||||| ||||||||||| |   |||||||||| ||||||||  ||    |||| |||| |     ||  | | |       | |    | |  | |  |                                        
AACGCACTGCTTCCTCAACTCTTACAAGAACGTTCTTGCTGTTGCTCTGGCGACTGATTACTCGTATCCACACGCCGAGACTGTCAAGGAGTATCTCAAGgtt-tgatcttttccttgt-catcagcaggtctctaacattctctcttccaacttttccag---------------------------------------

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|21809619|gb|BQ667937.1|BQ667937

EST:     AGACGGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAG                         GACCCGAGCAAGTTTGCTGTTGCTGCTCCTGTAGCTGCTGAGGACTCTAGT
genomic: AGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtg ... tggtttgcagGACCCGAGCAAGTTTGCTGTTGCTGCTCCTGTAGCTGCTGCGGACTCTAGT

EST: gi|32942953|gb|CF047772.1|CF047772

EST:     ACCCACACGCCGACAAGATCAAGGAGTACCTCAAG                         GACCCGAGCAAGTTTGCTGTTGCTGCTCCTGTAGCTGCTGCGGACTCTAGT
genomic: ACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtg ... tggtttgcagGACCCGAGCAAGTTTGCTGTTGCTGCTCCTGTAGCTGCTGCGGACTCTAGT

EST: gi|166618054|gb|EG302127.1|EG302127

EST:     CTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAG                         GACCCGAGCAAGTTTGCTGTTGCTGCTCCTGTAGCTGCTGCGGACTC
genomic: CTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtg ... tggtttgcagGACCCGAGCAAGTTTGCTGTTGCTGCTCCTGTAGCTGCTGCGGACTC

EST: gi|74239990|gb|DT647904.1|DT647904

EST:     AGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAG                         GACCCGAGCAAGTTTGCTGTTGCCTGCTCCTGTAGCTGCTGCGGACTCTAG
genomic: AGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtg ... tggtttgcagGACCCGAGCAAGTTTGCTGTTG-CTGCTCCTGTAGCTGCTGCGGACTCTAG

EST: gi|166411499|gb|EG308307.1|EG308307

EST:     AGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAG                         GACCCGAGCAAGTTTGCTGTTGC
genomic: AGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtg ... tggtttgcagGACCCGAGCAAGTTTGCTGTTGC

EST: gi|166693058|gb|EG202032.1|EG202032

EST:     GACTGACTACTCGTACCCACACGACCGACAAGATCAAGGAGTACCTCAAG                         GACCCGAGCAAGTTTGCTGTTGCTGCTCC
genomic: GACTGACTACTCGTACCCACACG-CCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtg ... tggtttgcagGACCCGAGCAAGTTTGCTGTTGCTGCTCC

EST: gi|89251150|gb|DY622936.1|DY622936

EST:     AGACTGACTACTCGTACCCACACGCCGACNAGATCAAGGAGTACCTCAAG                         GACCCGAGCAAGTTTGCTGTTGCTGCTCCTGTAGCTGCTGCGGACTCTAGT
genomic: AGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtg ... tggtttgcagGACCCGAGCAAGTTTGCTGTTGCTGCTCCTGTAGCTGCTGCGGACTCTAGT

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: 440

GCCCCACATGTTTATCAATGGGTACAAGAACGTGCTTGCTGTTGCTGTGGAGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtg ... tggtttgcagGACCCGAGCAAGTTTGCTGTTGCTGCTCCTGTAGCTGCTGCGGACTCTAGTGCTGCTGCTGCCCCCAAGGAGGAAGAGAAGGCTCCAGAGCCTGCCGAGG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 332

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 273

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCCACATGTTTATCAATGGGTACAAGAACGTGCTTGCTGTTGCTGTGGAGACTGACTACTCGTACCCACACGCCGACAAGATCAAGGAGTACCTCAAGgtagtgtgtgtttcattgtgccatgtcaattatttcgagcaatttaagtccatgtataaatctacttcatttaatcaccatgcttatcttcgaatttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG