ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctacttggggccatctgaatctgtcgggaatctgataggggcaagtctgcagtttagctgaccattttgttgtctaatgcatgctttag

Basic information

species	Zea mays
transcript	GRMZM2G157068_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 5'ss of exon 5

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt-ggggccatctgaatctgtcgggaatctgataggggc----aa-----gtctgcagttt-agctgaccattttgttgtctaatgcatgctttag------------------
||||||||||||||||| | ||||||||| |||||  ||||||| |||||||||||| ||||||| ||||| || |||||||| || ||   |  | | ||  | ||| |    | || || | ||    ||     |  |    ||| ||  |  |||     | |  | | ||| | ||                    
AACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAGgtatttatttcaagagcttttgcttatgt-gcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttcattactgtag

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G05440.1 (Glycine max), 5'ss of exon 5

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgt------atctacttggggccat-ctgaatctgtcgggaatctgataggggcaagtct----gcagtttag--ctgaccattttgttgtctaat---gcatgctttag----------------------------------------------
|| || ||||| ||||| | ||| || ||||||||  ||||||| |||||||||||||||||||||||||| || || |||      |  |  |      ||| || ||| | |      |    |     ||  | |    ||||  | |  ||     ||| ||||  | ||   ||||||| | |                                              
AATTTTCTTTTTAAATCAATCAAAGAAGATTCACCTTTAAAGGCCACAGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcag

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 7

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgta--------tcta----cttggggcca-------tctgaatctgtcgggaatctgataggggcaagtctgcagtttagctgaccattttgttgtctaatgcatgctttag-------------------------------------------------
|| || ||||| ||||| | ||| || ||||||||  ||||||| || ||||||||||||||||||||||| || || |||         |||      ||| || ||       |||   ||| |        |  | |   || |  ||   |     |       |||   | | | ||||||| | |                                                 
AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcag

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G37100.1 (Glycine max), 5'ss of exon 6

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctact--tggggccatctgaatctgt-cgggaatctgataggggcaagtctgcagtttagctgaccattttgttgtctaatgcatgctttag--------------------
|| || |||||||| || | ||| || ||||||||  ||||||| || |||||||||||||| |||||||| || || |||    |    || |   |||   |||| |       | | ||       ||  | ||   |       || | | || | | |   ||| |||                      
AATTTTCTTTTCAAGTCAACCAAAGAAGATTCACCTTTAAAGGCTACCGATTTTGGTTTGTCTGATTTCATAAAACCTGgtgagcaaaaatgtgttgatcattatctttgtttcctttttatccctcttagcattcaaaatgttcttgcaatct-ttatttgagttatggttttctctctttgcaaacaaaacag

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 5'ss of exon 5

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctacttggggccatctgaatctgtcgggaatctgataggggcaagtctgcagttta-gctgaccattttgttgtctaatgcatgctttag
|| || || |||||||| | | | || | |||| | |||||||| |||||||||||| |||| || ||||| ||||||||||   | ||       ||      ||||      ||||   | |||     | || | | |  |   |||||||     ||||   |      
AATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAGgtaaa-agtttcacttgtcaagtcttgtc-----cctga---gagcagaatggtagataatggaggtgattttgtgaa--aatggcag------

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|33096470|gb|CF056464.1|CF056464

EST:     TTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG                         GGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAG
genomic: TTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAG

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), 44 (downstream exon)
Score: 45

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 127

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214