ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G175321_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G175321_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g14100.1 (Oryza sativa), 5'ss of exon 1

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtgg--catccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcag
|| | |||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| |||| ||| ||||||||||||||||||||| |    ||| ||||   |||  |  |   | |  |     | || || |      | | ||     |||  |   | ||| |                                                                               
CCCGCAACGCCAAGTGGTGGTACTCCGCTTTCCACAACGTCACCGCCATGGTCGGCGCCGGCGTCCTCAGCCTCCCCTTCGCCATGTCCGAGCTCGGCTGgtacataattcattcatcatttctccttctccatttcatttcatcgtccatggatg---agtgttcgattttgtttttttttgtag-------------------------------------------------------------------------------

upper sequence: GRMZM2G175321_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G01300.1 (Glycine max), 5'ss of exon 1

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcag
|| | || |||||||||||||  || |||||||||||  |||| |||||||| || || || ||||||||||| || |  || |||||  |  | ||||||||| |||  ||       | |  | | |  | |  ||   |     ||    ||  | | |     | |  |    |     ||| | ||| |||  | ||| |||   |||  |                                               
CCCGAAATGCCAAATGGTGGTCTTCAGCCTTCCACAATCTCACAGCCATGGTTGGTGCAGGTGTCCTCAGCCTTCCATTTGCCATGTCAAATATGGGCTGgtacatggattc-------tttaatatcacctatcttctgaga---aattattatatagtttgaaatcatata---gttaaaggtcccaatcaatc--tctaagtgac--atgtttt----------------------------------------------

upper sequence: GRMZM2G175321_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G10740.1 (Glycine max), 5'ss of exon 1

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggcatccatctgatct---ggtcttaattgttgtcctcgcctcgat-cggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcag
|| | || ||||||||||||||||| |||||||||||| |||| |||||||| || || || ||||||| ||| || || || |||||   | | ||||||||| |  |||||   | | ||        | |||||        ||| |   |    || || ||||   |||   |  || ||   ||    | |   || ||   ||||  ||  | |                                              
CCCGAAATGCCAAATGGTGGTACTCTGCCTTCCACAACATCACTGCCATGGTTGGTGCTGGTGTCCTCACCCTTCCTTATGCCATGTCTATGATGGGCTGgtaccta-catcctcttaaactttaaactatgattgtaacttgtacctagtcacactttgaaaaattgatgctt---tatatatgatatcaaattagcaacaattg--tgatgcattaacag---------------------------------------------

upper sequence: GRMZM2G175321_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G27770.1 (Glycine max), 5'ss of exon 1

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatt-taactgatcgatggata-tatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcag
     || ||||||||||||||||| |||||||||||| |||| |||||||| || || || |||||||  || || || || |||||   | | || ||||||||  | |||   | | ||    | || | |  | ||  | |  | |      || | |       ||| | ||| | | |   |||| ||| | || ||  ||||       ||  ||| ||     ||| | ||| |                       
----AAATGCCAAATGGTGGTACTCAGCCTTCCACAACATCACCGCCATGGTTGGTGCTGGTGTCCTCACTCTTCCTTATGCCATGTCTATGATGGGTTGGTACgta-cgtcctcttaaact---ttaaactatgatgctaacttgtacctagtcacactttcaatgactgcgt-catatattga-acgattgatgctttatagatgatatggaattaacatgaattgtgttgcattaacaag----------------------

upper sequence: GRMZM2G175321_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT1G24400.1 (Arabidopsis thaliana), 5'ss of exon 1

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggcatccatctgatctggt---cttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcag
|||| ||||| || ||||||||||| || || ||||| ||||| |||||||| || || || || || ||| |||||||||| |||||| | ||||| |||||      ||   |   ||||| |   ||||||  |  |    |  |  |||      |     || |  ||  ||| || |   |                                                                               
CCAGAAACGCTAAGTGGTGGTACTCTGCTTTTCACAATGTCACCGCCATGGTTGGTGCTGGTGTTCTTAGCTTGCCCTACGCTATGTCCAATCTCGGATGgtatacta-atttgttgaatctgataatcttaatc-tcctttatgttttaatccatgatctgatctgagtttttgatgtat-tacag-------------------------------------------------------------------------------

upper sequence: GRMZM2G175321_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S5_176V6.1 (Physcomitrella patens), 5'ss of exon 2

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcag
   | || ||||||||||||||||||||||||||||| || || || ||||| |||||||| || ||  |  ||||| |||| |||  | |  |    ||||  | |     | ||   | | |||| |           || |||    | ||  || | |  ||       ||||  |  ||  ||  | |   ||  |||| ||   |||| |||    ||                                       
ATCGCAAAGCCAAATGGTGGTACTCCGCCTTCCACAATGTTACCGCAATGGTGGGCGCCGGAGTGCTGGGATTGCCCAACGCCATGGTCTACTTAACATGgtgaggg---ctcctcacgttttgtctaa---------tccgtctcaga-gtcacacagtttcatgt------tgcagtttgcg--gcagtgggcacaagtaacgga---atggctattcacatgcag-----------------------------------

upper sequence: GRMZM2G175321_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ10949 (Selaginella moellendorffii), 5'ss of exon 1

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcag
| |||||||||||||||||||||||||| || |||||||| || || ||||| ||  | ||||| ||     | ||||  || |||    | || || |||||    |     || | ||   ||||  ||| ||       | ||| |   |  |                                                                                                           
CGAGGAACGCCAAATGGTGGTACTCCGCGTTTCACAACGTAACCGCGATGGTAGGATCGGGCGTGCTGGCGTTACCCTCGGCTATGGTTTATCTGGGATGgtaa--cgttcgaatgttataacgtctacattttttagggttcttcgtttttccag-----------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G175321_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ10950 (Selaginella moellendorffii), 5'ss of exon 2

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggcatccatctgatctg-gtcttaattgttgtcctcgc-ctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcag
||||||||||||| ||||||||||| |||||||| || ||||| |||||||| || || || || || ||||| ||||  || |||  | | || |||||||| ||      || ||  |||  || | ||| | |  | ||    ||| |  |  |  |      | | | |   |    |||  || |  |||  |                                                                   
CCAGGAACGCCAAGTGGTGGTACTCGGCCTTCCATAATGTCACCGCCATGGTTGGAGCTGGAGTTCTTAGCCTCCCCTCGGCGATGGTCTATCTTGGCTGgtaagttcttcgcagctcttcttcgtttcaatcgctagcttcaaattcgcttagtttcgatccaaattcttggtcagtcagtgttttctcattcgtgctc-----------------------------------------------------------------

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|211471200|gb|FL264979.1|FL264979

EST:     GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC

EST: gi|211471202|gb|FL264981.1|FL264981

EST:     GTCGG-TCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC

EST: gi|149010013|gb|EE041826.2|EE041826

EST:     GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC

EST: gi|211471201|gb|FL264980.1|FL264980

EST:     GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC

EST: gi|211471204|gb|FL264983.1|FL264983

EST:     GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGC-ATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC

EST: gi|211471203|gb|FL264982.1|FL264982

EST:     GTCGG-TCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC

EST: gi|211471199|gb|FL264978.1|FL264978

EST:     GTCGGT-CCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGC-ATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC

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 2 RNA-Seq libraries.

Block sizes: 9 (upstream exon), 41 (downstream exon)
Score: 1

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC