ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGTCTCCTCCTCTGTCGGACCCGAGTACTATGTCAGCATCCTCTCCTTTGTCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttctacttgccagggacccgcgctactacccggagcggatctagcatcctcgatctaaatatctccctccgatctagtcgttggatgtgtagac...

Basic information

species	Zea mays
transcript	GRMZM2G095593_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 5'ss of exon 1

CGTCTCCTCCTCTGTCGGACCCGAGTACTATGTCAGCATCCTCTCCTTTGTCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgt-ttgtttct-acttgccagggacccgcgctactacccggagcggatctagcatcctcgatctaaatatctccctccgatctagtcgttggatgtgtagac-
|||||||||||| ||||| ||||||||||| ||| ||||||||||||| ||||||||||||||||||||||| || |||||||||||||||||||| |||||  |  | || ||   |||  |     |||  | | |     ||| ||   ||    |  | ||       | || | |  || ||    | | |  |||  
CGTCTCCTCCTCCGTCGGCCCCGAGTACTACGTCGGCATCCTCTCCTTCGTCGACAAGGACCAGCTCGAGCCCGGCTGCTCCATCCTCATGCACAACAAGgtactactgctcaccccccatcgctttccgcatcgatctacttcggttcatacacatac--tttaggccggcctcttccacataatcaaaag-tattaagatc

upper sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 1

CGTCTCCTCCTCTGTCGGACCCGAGTACTATGTCAGCATCCTCTCCTTTGTCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttg--tttctacttgccagggacccgc-gctactacccggagcggatctagcatcctcgatctaaatatctccctccgatctagtcgttggatgtgtagac
||| || || || || || |||||||| ||||| | |||  | || || || |||||||| ||||||||||| || ||| | |||||||||||||||||||| ||  || | |  |   ||       | |||  |   |    |   |    |||   | | |   | |      ||      | | | | ||  |||    
CGTTTCGTCTTCCGTGGGGCCCGAGTATTATGTGAACATTTTGTCGTTCGTGGACAAGGATCAGCTCGAGCCCGGTTGCGCAATCCTCATGCACAATAAGgtatgccttcccaaatctaagaagttttcagcttatttgctcttcaatttcttcattgccaaaccctaaactatgttctatcacacttgctaga-atgtcc--

upper sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 5'ss of exon 1

CGTCTCCTCCTCTGTCGGACCCGAGTACTATGTCAGCATCCTCTCCTTTGTCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttctacttgccagggacccgcgctactacccggagcggatctagcatcctcgatctaaatatctccctccgat--ctagtcg---ttggatgtgtagac
 || || || || || || || ||||| ||||| |  ||  | || || || |||||||| ||||||||||| || ||| | |||||||||||||| |||||  |     |  | |   ||     |  | ||             || || |  | | |  || |   || ||  |||   | || |   ||  || ||   | 
TGTGTCATCGTCCGTGGGTCCTGAGTATTATGTGAATATTTTATCGTTCGTGGACAAGGATCAGCTCGAGCCTGGTTGCGCAATCCTCATGCACAACAAGgtgcg-----atcttctgaggcttatcattgcttattttttttccactcgcttggttgtttcaacttattctctaggatagttggtagggtttcaatatgcgcaa

upper sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ32659 (Selaginella moellendorffii), 5'ss of exon 1

CGTCTCCTCCTCTGTCGGACCCGAGTACTATGTCAGCATCCTCTCCTTTGTCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgt-ttgttt--ctacttgccagggacccgcgctactacccggagcggatctagcatcctcgatctaaatatctccctccgatctagtcgttggatgtgtagac
 || || || || ||||| || ||||||||||||| ||| || || ||||| |||||||||||||| ||||| || ||  | ||||||||||||||||||||  |||||  || ||||| || |      | | ||||   |      |   |||                                                
TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTTGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgttttcctgcttgctagcg---tttgtttctactttgtttctcttcggcag-----------------------------------------------

upper sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 1

CGTCTCCTCCTCTGTCGGACCCGAGTACTATGTCAGCATCCTCTCCTTTGTCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgt-ttgtttc-tacttgccagggacccgcgctactacccggagcggatctagcatcctcgatctaaatatctccctccgatctagtcgttggatgtgtagac
 || || || || ||||| || ||||||||||||| ||| || || || || |||||||||||||| ||||| || ||  | ||||||||||||||||||||  |||||| | ||||| || |      | | ||||   |      |   |||                                                
TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttcctgcttgctagcg---tttgtttctactttgtttctcttcggcag-----------------------------------------------

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|32805273|gb|CD957509.1|CD957509

EST:     TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAG                         GTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT
genomic: TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttct ... tactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT

EST: gi|32938600|gb|CF043419.1|CF043419

EST:     TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAG                         GTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT
genomic: TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttct ... tactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT

EST: gi|37419302|gb|CF647331.1|CF647331

EST:     CATGCACAATAAG                         GTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT
genomic: CATGCACAATAAGgtttgtttct ... tactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT

EST: gi|19272515|gb|BM888771.1|BM888771

EST:     AAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCGCAATAAG                         GTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT
genomic: AAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttct ... tactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT

EST: gi|32941761|gb|CF046580.1|CF046580

EST:     TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAG                         GTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT
genomic: TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttct ... tactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT

EST: gi|32836748|gb|CD976426.1|CD976426

EST:     TCGACAAGGACCAGCTCGAGCCGGTATGCTCCATCTTCATGCACAATAAG                         GTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT
genomic: TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttct ... tactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT

EST: gi|32790190|gb|CD942426.1|CD942426

EST:     TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAG                         GTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT
genomic: TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttct ... tactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT

EST: gi|78119973|gb|DV538357.1|DV538357

EST:     TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAG                         GTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT
genomic: TCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttct ... tactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCT

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: 602

CGTCTCCTCCTCTGTCGGACCCGAGTACTATGTCAGCATCCTCTCCTTTGTCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttct ... tactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCACCTTTGGAATCTTATGCTGACATTGGTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 610

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 766

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 628

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCTCCTCCTCTGTCGGACCCGAGTACTATGTCAGCATCCTCTCCTTTGTCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgtttgtttctacttgccagggacccgcgctactacccggagcggatctagcatcctcgatctaaatatctccctccgatctagtcgttggatgtgtagac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccgcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctcc