ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCAAGGCCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttctcttcaactctgaagcctatattaactacacaactatctgcaatatgatgaaactttgtgcttcttgctttttctttgacaaatgagtgattttgcag

Basic information

species	Zea mays
transcript	GRMZM2G103047_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G103047_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 5'ss of exon 3

AAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCAAGGCCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc--tcttcaactctgaagccta-tattaactacacaactatctgcaatatgatgaaa-ctttgtgcttcttgctttttctttgacaaatgagtgattttgcag
 ||||||||||||||||||||||| |||||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||| ||||||| || ||||||| | ||   | |||  | |||  ||| | |  ||||||  ||||    |  ||| | |  ||| |  | || |||||| |||   | | | | || | | | |||||||
GAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATCAAGGCTATGGAGCCTTTCTTTTCAGTTCTGCTTTCAGCACTTTTCCTCGGAGAGgtaattttttaatgttctgcactggtgcccagtgataactatgcaaccgcatataatcttagaaaaaccatctgtttcttggtttggttctcatacataa-tcactttgcag

upper sequence: GRMZM2G103047_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3

AAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCAAGGCCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttctcttcaactctgaagcctatattaactacacaactatctgcaatatgatgaaactttgtgcttcttgctttttctttgacaaatgagtgattttgcag
 ||||||||||||||||||||||||||||||||||| || || |||||||| ||||| || || ||||| ||||| || || || || |||||||| |||||| |     |   ||     |    |||||| || | |       | ||||                                                        
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgatacgttcgcagaaaaggt-tctatatcaattgcc------tttgcag-------------------------------------------------------

upper sequence: GRMZM2G103047_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 3

AAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCAAGGCCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttctcttcaactctgaagcctatattaactacacaactatctgcaatatgatgaaactttgtgcttcttgctttttctttgacaaatgagtgattttgcag
 ||||||||||||||||||||||||||||| ||||| || || |||||||| ||||| || || ||||| ||||| || || || || |||||||| |||||| |     |   ||     |    |||||| |  | |       | ||||                                                        
CAACATGAGCCTTGGAAAGGTTGCGGTGTCGTTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgatacgttcgcagaaaaggt-tctatatcagttgcc------tttgcag-------------------------------------------------------

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|148999234|gb|EE036154.2|EE036154

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|60349997|gb|DN216970.1|DN216970

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|21760182|gb|BQ635723.1|BQ635723

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|76916104|gb|DV166241.1|DV166241

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|74235578|gb|DT643492.1|DT643492

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|9794211|gb|BE552519.1|BE552519

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|60349346|gb|DN216319.1|DN216319

EST:     GCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: GCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|149072472|gb|EE160748.2|EE160748

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|71444331|gb|DR825381.1|DR825381

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCATTTTTC-TTGGTGAG                         TTGCCTACGCCTTGGGGTGGTGTTGTCTCTTC
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTG-TGTTGTCTCTTC

EST: gi|149094831|gb|EE180400.2|EE180400

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGT
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGT

EST: gi|26457500|gb|CA829083.1|CA829083

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|4753301|gb|AI657206.1|AI657206

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATTGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|31358649|gb|CD443006.1|CD443006

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGGTTGTGTTGGCTCTTCTTCCGATCGTTGGGGGTGT
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGG-TTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGT

EST: gi|78110415|gb|DV528827.1|DV528827

EST:     CCATGGAACCTTTCGTCTCGGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

EST: gi|149007367|gb|EE040217.2|EE040217

EST:     CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAG                         TTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG
genomic: CCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTG

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), 49 (downstream exon)
Score: 280

AAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCAAGGCCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttc ... gattttgcagTTGCCTACGCCTTGGGTTGTGTTGTCTCTTCTTCCGATCGTTGGTGGTGTGGCATTGGCATCCCTTACTGAGGCCTCCTTTAACTG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 267

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 343

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 339

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCAAGGCCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttctcttcaactctgaagcctatattaactacacaactatctgcaatatgatgaaactttgtgcttcttgctttttctttgacaaatgagtgattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA