ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcggcaacttttttctgtctactggatctaatctatatatccttgtttcatacacgtttcaaatgtacag

Basic information

species	Zea mays
transcript	GRMZM2G152686_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 4

GAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcggcaacttttttctgtctactggatctaatctatatatccttgtttcatacacgttt--caaatgtacag
|||||||| || ||||||||||||||||| || |||||| ||||||| ||||| || |||||||||||||||||||| |||||||||||||||||||||||||||||||  ||      |||  |  |||| || | ||  | | |  |||||||||| | | |||    ||  | |||
GAAGATTCGGTAAAATGTGAAGTTATTGATGGAGGTGAACTGAAATCCAGGCGTCACCTGAATGTTCGTGGAAAGAGCGCAACCTTGCCATCAATAACTGgtaatagtcaaca------ttcatttcactgaatattat--aaacactcttgtttcattctcattttctgaacttgcag

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 5'ss of exon 4

GAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcggcaactt--ttttctgtctactggatctaatctatatatcct---tgtttcatac--acgtttcaaatgtacag---------------------------------------
 |||| ||||| |||||||||||| |||| ||||| ||| | || || ||| | || |||||||| || |||||||||||||| || || ||||| ||||||   | |   |   ||    |  | |  |||   |||  |   | |        |||| ||||   | || | |||  |                                           
AAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTGgttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcag

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 4

GAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcggca--acttttttctgtctactggatctaatctatatatccttgtttcatacacgttt---caaatgtacag---
| |||||| ||||||||||||||| |||| ||||| ||| | || |||||  | ||||| |||||||| ||||| ||||||||  |||||||||| ||||||   |   || |  | |      ||| ||  | |  |  | | | |  |  |     |||    |||      || | | |   
GGAGATTCAGTGAAATGTGAAGTTGTTGATGGTGGAGAACTCAAGTCTAGAAGGCATCTAAATGTTCGAGGAAAAAGTGCAACACTGCCATCAATTACTGgttggacatggaatgagtccccaatgtttatagcaaatgctttgttttgcaattcaaaataacaatttgctttgatttgctgcag

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|5296084|gb|AI782959.1|AI782959

EST:     GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTG                         ACAAGGACTGGGACGACATTAAGTTTGGNGTGGATAATCAAGTTGATTACT
genomic: GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT

EST: gi|71426208|gb|DR807258.1|DR807258

EST:     CGCCATCTGAATGTTCGTGGGAAGAGTGCAACCTTGCCATNCA-TAACTG                         ACAAGGACTGGGACG
genomic: CGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCAT-CAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACG

EST: gi|211141481|gb|FL154590.1|FL154590

EST:     GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTG                         ACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT
genomic: GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT

EST: gi|67025561|gb|CO454310.1|CO454310

EST:     GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTG                         ACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT
genomic: GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT

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), 48 (downstream exon)
Score: 444

GAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 343

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 220