ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaatctttgtgataaattcggcttcaattcgcagttttagcaaacaagttcatcaaacagcttgttgaatgttacactgtag

Basic information

species	Zea mays
transcript	GRMZM2G058702_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 2

GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaatctttgtgataaattcggcttcaattcgcagttttagcaaacaagttcatcaaacagcttgttgaatgttacactgtag
|||||| ||||||||||| |||||||  ||||||||||| || |||||||| ||||| |||||||| || ||||||||||||||  |||||||||| |||||||     |||| |||| | |||   | |||| || | | ||  | || |  ||||||   || ||||||   ||||  |   || ||
GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggatatctgtgtgtttaatgtcgtttcatttaggaattgaatcatatgagttcactgaatagcttgagcaatggcatgatgcag

upper sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA20G24830.1 (Glycine max), 5'ss of exon 2

GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgt------acaatcttt--gtgata-------aattcggcttcaattcgcagttttag---caaacaagttcatcaaacagctt----gttgaatgttacactgtag-----------------------------------------------------------------------------------
 || || ||||  |||   || ||| ||||||||||  |||| || |||||||||||| |||||||  | || || ||||||||||||||||| || |||||  ||      || ||| |   |  |||        ||||   |  ||||  | ||   |    | ||| | || ||| | |    |    ||  |||| ||   ||                                                                                      
AGACGGCAAGAATTTCGTGTATAACGGTAACATCAATGTTGCTGTTGCTGTGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggcttgactatcctgaagcaatattatggtgattcatgtctaattttctgtgccatactccaactatttgatctatctttatctgagtccaatggtatcttgcgagcaatccatgtagctgacctctcctgattgttgtttttgtctaatttgttatttgattgggtacttgtttcttgttgtgacag

upper sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G20720.1 (Glycine max), 5'ss of exon 2

GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgta-----caatctttgtgataaattcggcttcaattcgcagttttagcaaacaagttcatcaaacagcttgttgaatgttacactgtag----------------
 ||||| |||| |||  | || || |||||||| |||||||| || ||||||||||   |||||||  | |||||||| |||||||||||||| || |||||| ||        |  |   | ||   |  |  |   |   | | ||  || | ||||  |  |    ||| |  ||   |  |    ||                   
AGATGGGAAGAACTTTGCCTATAATAGTAACATTAACATTGCTGTTGCTGTGGCAACCAATGGTGGTTTGATTACACCGGTTCTTCAGGATGCAGATAAGgtatgtgattagtgaattggataattgttctgaatcagaacagtaattggagaatacaaaattgtgtttcagttccttagttaattgtttgcttacttgttttgttacag

upper sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G25860.1 (Arabidopsis thaliana), 5'ss of exon 2

GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaatctttgtgat-----aaattcggcttcaattcgcagttttagcaaacaagttc------atcaaacagcttgttgaatgttacactgtag----------------------
 || || ||||| || |  ||||| |||| ||| |||||||||||||| || || ||  |||||||||| ||||| |||||||| || ||||| || |||||| | | || |  |    |     ||| | |    |   |    |  ||| || |||   |       || |  | | ||  |  |  | |   |||                        
AGACGGGAAGAGTTTTAGTTACAATAGTAGCATTAACATTGCAGTGGCGGTTGCTATCAATGGTGGCCTGATTACGCCTGTTCTACAAGATGCAGATAAGgtaagcataagcaataaagttgtagaaaatagctagcgtgtgagtgaattaacacacacacttggtattattaggctggtttctttaactgaatgtgtgagtcgtgttggttgttttgatag

upper sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 2

GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgta-----cgtacaatctttgtgataaattcggcttcaattcgcagttttagcaaacaagttcatcaaacagcttgttgaatgttacactgtag------------------------------------
 ||||| ||||  || ||||| ||||| |  || |||||||| || || ||||||||  |||||||  | || || |||||||||||||||||||| ||||||     | | || | | ||||  |||||||     || |    || |   |   ||||||     ||     | |||| | |||   |  |                                     
AGATGGGAAGACTTTTACATATAACAGCAGTATAAACATTGCGGTAGCAGTGGCAATCAATGGTGGGTTGATAACCCCTGTTCTTCAGGATGCTGATAAGgtaaatgacatgcattttctgtgg-aaattcgtgaaaaaattcttgtatc--ctgtcaagtt--atgaatgatgttttgatttttaatttcgaaattagtttagttaataatttgtttttgatggtgtag

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|67018197|gb|CO446946.1|CO446946

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|78114407|gb|DV532796.1|DV532796

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|67011881|gb|CO440630.1|CO440630

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|78027609|gb|DV495996.1|DV495996

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|91054582|gb|EB165000.1|EB165000

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|211115866|gb|FL470201.1|FL470201

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|32939307|gb|CF044126.1|CF044126

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|148943508|gb|EC888569.2|EC888569

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|31349054|gb|CD433411.1|CD433411

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|32942394|gb|CF047213.1|CF047213

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTC--GCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|4827706|gb|AI668398.1|AI668398

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|71432412|gb|DR813462.1|DR813462

EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

EST: gi|6827927|gb|AW331570.1|AW331570

EST:     TGGCAATTGATGGTGGCCTTATTACCCCTGTTTTTCAGGATGCTGACAAG                         CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCC
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCA

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: 45 (upstream exon), 49 (downstream exon)
Score: 72

GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaa ... tacactgtagCTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 38

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 137

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgtacaatctttgtgataaattcggcttcaattcgcagttttagcaaacaagttcatcaaacagcttgttgaatgttacactgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG