ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccag

Basic information

species	Zea mays
transcript	GRMZM2G042074_T02
intron #	17
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 22

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatag-catctaaataacctattttccag--------
|||||| |||||||| ||||||||||||||||| || |||||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||||||||||||| ||    | |  |  |    || ||  |     |||  || | |||||| | | ||||| ||  |  | | | |||         
TGGCCCGCCTGGTACAGGAAAGACAATGCTTGCCAAAGCTGTGGCTACAGAGGCTGGTGCGAATTTCATAAATATATCAATGTCGAGCATCTCTTCAAAGgtatttt---actaaatga-ttgctattagtccatggttttgtttttgcattttgggcatctgaaacat-tgtgtaccattaccacag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA06G17940.1 (Glycine max), 5'ss of exon 22

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgt-----acttatcaattggacaa-------gcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccag
||| || ||||| || || |||||||||||||| ||||| || || || || |||||||| |||||||| ||||| || |||||||| ||| | || |||||     |    ||| | ||   |       | ||||||| |  |  |||||   || |  | |  |   | |    |   |  ||  |||
TGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgttagatatgcttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccattttgctt--cag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 21

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggacaagcctctgttttttggcagttgagtatctgcatta-tagcatctaaataacctattttccag------
||| || ||||| || ||||| ||||||||||| |||||||| |||||||| ||||| || |||||||| ||||| || ||||| |||||  ||||||||||| | ||    |     |   | | || |   | | ||   | | ||| | | |  ||   |||  |    |||    |      
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtattaatgttgtaagttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttgttgcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 20

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgt---acttatc-------aattggacaagcctctgttttttggcagttga--gtatctgcattatagcatctaaataacctattttccag
||| || ||||| ||||| || ||||||||||| |||||  | || ||||| ||||||||||| ||||| ||||| || |||||||| ||| | || |||||   | || ||       || || | |    | |    |||   ||||    ||   | ||    |   |||        | |  | |||
TGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTTCTATGTCAAGTATCACATCTAAGgttaaatttgtctctctctaagtgtatattgatttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 18

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatc----aattggacaagcctctgttttttggcagttgagtatc-tgcattatagcatctaaataacctattttc----cag
|||||| ||||| || ||||| ||||||||||| ||||||||||||||||| ||||| || ||||| || ||||| || ||||| |||||  | || |||||| |  |     | ||  ||     |    |  |  | | ||   | || | ||||| ||   |   |||   | ||||     |||
TGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTTCAATGTCCAGCATTACATCCAAGgtattagttgcaaatttaaactgttttgctctactctgtattttcctttcattcatta-agtgacaggatattgtttttttgttgcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 5

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgt---actta-tcaattggacaagcctctgttttttggcagttgagtatctg--cattatagc-atctaaataacctattttccag---
||| || ||||| || || |||||||||||||| ||||| || || || || |||||||| |||||||| ||||| || |||||||| ||| | || |||||   | ||  |  | |||       |   | | |  ||  |    ||  ||  |||| || |  | |   |  || ||||| |     
TGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgttaaatttgcttcactgggtttattttaatgtctctgctatcagttagttgttcattttatctgtgttcttttcccattttgcttcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 17

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggacaagcctctgttttttg-gcagttgagtatctgc----attatagcatctaaataacctattttccag---
||| || ||||| || ||||| ||||||||||| |||||||| |||||||| ||||| || |||||||| ||||| || ||||| |||||  |||||||||||   ||  |||| | |   || | ||| ||| | | ||   | | |||     ||| |  |   | ||    |  |||   |   
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtatcaat--attgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgtttgttgcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 18

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatc----aattggacaagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccag------
|||||| ||||| || ||||| ||||||||||| |||||||| |||||||| ||||| || ||||| || ||||| || ||||| |||||  | || |||||| |  |     | ||  |||    |    |  || | | ||   |   | ||| |  |     | | |   | ||||   |      
TGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTTCAATGTCCAGCATTACGTCCAAGgtattagttgcaaatttaaacagttttgctctactttgtatttcctttcattcataagtgacaggatagatattgtttttttgttgcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 21

------------TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctatt-ttccag
            ||| ||  |||| ||||||||||| |||||||| ||||| |||||||| || |||||||||||  |||| ||||| || ||||||||  |  |    |   ||    | ||        | ||||     ||   |   |          ||  | | | |      |  | | || |||
AATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGTCAATGTCAAGGgtaac----agaatatccttgaa--aagttggactctaccaatttatacacggaatctcttgttcaaacttgtgttcttctcaatattgcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 21

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgta---cttatcaattgg-acaagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccag
||| || ||||||||||||||||| ||||| || || || || |||||||||||||| || |||||||| || || || ||||| |||||  |||| ||||||   || || || ||  |  |    || || |       || | |   || | |  | ||| || |  |  |  ||| |||
TGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCTCAATGTCCAGCATTACTTCGAAGgtaactctcataaagtgatatgatttccttttatgctttcttttaatgattgtacttgaccatttacactaaatgctttgcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggac--aagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctatt-ttccag
||| || ||||| ||||||||||| |||||||| || || |||||||  || |||| ||| || ||||| ||||| || |||||||||||| | || ||||||  |    | |  |   ||   |||     ||  ||   | |    |   ||  | | | |      | || |  | |||
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccag--------------------------
|||||| ||||| || || ||||||||||||||||||||||| || ||||| |||||||| || ||||| || || || |||||||||||| | || |||||  | ||  ||  |   ||| ||| |||| |  |  ||||   |||  ||  | |  | | | |    | |||  |||                          
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagt--agcttcttttttctatcccttga---tctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 21

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttat------caat----tggacaagcctctgttttttggcagttgagtatctgcattat--agcatctaaataacctattttccag
||| || ||||| |||||||| ||||||||||| ||||| || ||||||||||| ||||| ||||| || |||||||| ||||| || ||| |||||||||||  |||      |||     ||   | ||  || | |||||  |||   || |    | |||    ||||   |||   |   || |||
TGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATATCAATGTCTAGTATCACTTCAAAGgtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgata---ttgcttgcag

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: PP1S3_184V6.1 (Physcomitrella patens), 5'ss of exon 18

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaatt-----ggacaagcctctgttttttggcagttg--agtatctgcattatagcatctaaata-acctat---tttccag----------
||| ||||| ||||| || ||||| ||| | ||||||||||| |||||||| || || ||||| ||||||||||| || ||||| | |||  |||| ||||| ||| |   ||     | |     ||  | | ||    ||| |  | | |     | ||   ||   |||| |  ||    ||| |||          
TGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTTCCATGTCTACCATTGCTTCCAAGgtgctttttggttttttcgaaagttgctacgatgttgaagagtagtcaatgttcaactcatgaaattataatatatgtagacattttcagttgctccaca

upper sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
lower sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccag
||| || || || ||||| ||||| |||||||||||||| || || || ||||||||||| |||||||| || || || ||||| |  ||  | || || |||   |   |       |   | |     ||  | |||   | ||| |                              
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcag--------------------------

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|67017525|gb|CO446274.1|CO446274

EST:     AGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAG                         TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGT
genomic: AGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatca ... tattttccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGT

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: 147

TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatca ... tattttccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 247

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152