ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttccttgctttttttcaagaagaatatgtttctggaatatctcttagcaatttccttgcatcacactgccttttggtacaatgtttgtgatgat...

Basic information

species	Zea mays
transcript	GRMZM2G054634_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G054634_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 5'ss of exon 6

GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttc--------cttgctttttttcaagaagaatatgtttctggaatatctcttagcaatttccttgcatcacactgccttttggtacaatgtttgtgatgat
||||||| ||  | ||||||||||| |||||||||||||| || || |||||||||||||| || || ||||| |||||||| ||||||||||||        | |   |||| |||||||  |||| | || |   |    |||| || |   ||   |||           ||   |  | |||        
GCAGAGTCATCGCCGAGAGTGTGATATATAGCTATGGAACAGTTCTTTTGGATCTTTTGAGTGGGAAGCACATACCTCCTAGCCATgtatgcttcgtttaaatccttacttttctcaagaaatatatatatcagcgcttctccttatcattactctcatatcctggataacactgcatctgtattt--------

upper sequence: GRMZM2G054634_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA17G16420.1 (Glycine max), 5'ss of exon 6

GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttccttgctttttttcaagaagaatatgtttctggaat-atctcttagcaatttccttgcatcacactgccttttggtaca----atgtttgtgatgat---
||||  |||| || |||||||||||||| || ||||||||||| ||  |||||||||| || || || ||||||||||| || ||||||||     |||| || |   ||||| | |  || |||| | | || |   | ||   |   ||  | |  |||  |  |   |||    | |  |   ||| |   
GCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTTTAAGTGGCAAGCACATTCCTCCAAGCCATgtatg-----ttgcgttct---aagaaaattcagtctctgcattcatataagaacatgctttatgttttattctgtttcataagacatgataagcattctatgttacc

upper sequence: GRMZM2G054634_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G06140.1 (Glycine max), 5'ss of exon 6

GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttccttgcttttt--ttcaagaagaatatgtttctg-gaatatctcttagcaatttccttgcatcacactgccttttggtacaatgtttgtgatgat
||||  |||| || |||||||||||||| || ||||||||||| ||  |||||||| | || || || || |||||||| || |||||||| | | ||         | ||        ||   | |  |||| |   |||    ||   |||  ||| |  || || |    || | | ||| |    
GCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCATgtatgttgcgttctaacaaaatccagtctctgcattcatataagaatgtgctttatgctttattttgtttcataaggcattataa-gcattctatgttacc--

upper sequence: GRMZM2G054634_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT5G46570.1 (Arabidopsis thaliana), 5'ss of exon 5

GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatg--cttcc------ttgctttttttcaagaagaatatgtttctggaatatctcttagcaatttccttgca-tcacactgcctt--ttggta-caatgtttgtgatgat
| ||||| ||||| || |||||||| |  || ||||||||| | || || |||||||| ||||| ||||||||||| ||||| ||||||||  |||||       |  |||  ||||       |   ||| | |   ||  |  || | |||  |||   ||    |  ||   |||||    ||||||   || | 
GTAGAGTCATTCCTGAAAGTGTGATATTCAGTTATGGAACTATTCTTTTAGATCTTTTAAGCGGCAAACACATTCCACCTAGCCATgtatgtgcttccaatgttctaatttccttcattttatcttacttttttgtcaattgccgaggattttatttgtggtcttcttatctgaattggtggtgatgtttcatatcag

upper sequence: GRMZM2G054634_T02 (Zea mays), 5'ss of exon 6
lower sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 5

GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgta--tgcttccttgctttttttcaagaagaatatgtttctggaatatctcttagcaatttccttgcatcacactgccttttggtacaatgtttgtgatgat
| |||||||  || |||||||| || ||||| ||||| ||||| || ||||||||| | ||||| || ||||||||||| || || ||   || |||   |||  | ||     ||  | ||  | || |||         |    |   ||||                                  
GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagtgattcaaagctcctctt-----agcttgtgagtttgtaatcctgtgcttcttcatgtgtgcag---------------------------------

upper sequence: GRMZM2G054634_T02 (Zea mays), 5'ss of exon 6
lower sequence: EFJ23298 (Selaginella moellendorffii), 5'ss of exon 5

GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgta--tgcttccttgctttttttcaagaagaatatgtttctggaatatctcttagcaatttccttgcatcacactgccttttggtacaatgtttgtgatgat
| |||||||  || |||||||| || ||||| ||||| ||||| || ||||||||| | ||||| || ||||||||||| || || |||  || |||   |||  | ||     ||  | ||  | || |||         |    |   ||||                                  
GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtaagtgattcaaagctcctctt-----agcttgtgagtttgtaatcctgtgcttcttcatgtgtgcag---------------------------------

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|89248037|gb|DY619823.1|DY619823

EST:     GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT                         GCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC
genomic: GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttcc ... ggaattctagGCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC

EST: gi|211485328|gb|FL295172.1|FL295172

EST:     GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT                         GCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC
genomic: GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttcc ... ggaattctagGCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC

EST: gi|211485330|gb|FL295174.1|FL295174

EST:     GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT                         GCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC
genomic: GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttcc ... ggaattctagGCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC

EST: gi|211485329|gb|FL295173.1|FL295173

EST:     GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT                         GCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC
genomic: GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttcc ... ggaattctagGCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC

EST: gi|71439297|gb|DR820347.1|DR820347

EST:     GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT                         GCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC
genomic: GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttcc ... ggaattctagGCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC

EST: gi|78122641|gb|DV541025.1|DV541025

EST:     GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT                         GCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC
genomic: GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttcc ... ggaattctagGCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC

EST: gi|32930139|gb|CF034951.1|CF034951

EST:     GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT                         GCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC
genomic: GAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttcc ... ggaattctagGCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCC

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: 220

GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttcc ... ggaattctagGCCCTAGATTTAATAAGGGGAAAGAATATACTGTTGCTGATGGATTCCTCCTTAGAAGGGCAGTATGCTAATGAAGATGCTTCGAAATTGGTTGATCTTG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 17

Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 6