ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatatgcttagtttagttcattttcatccatttttttatctgctgtttctacgacggaagcattattcaaggtgactaattaaaagctcatcgatcagtggctgaggataccatggcatgcttttgcttggatgtag

Basic information

species	Zea mays
transcript	GRMZM2G445478_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G445478_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g32910.1 (Oryza sativa), 5'ss of exon 5

GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatatgcttagtttagttcattttcatccatttttttat-ctgctgtttctac-gacggaagcattattca-aggtgactaattaaaagctcatcgatcagtggctgaggataccatggcatgcttttgcttggatgtag
||||||||  ||||||| |||||||||||| | || || |  |||||||| ||||||||||| || || ||||| || ||||||||||||||||||| || |  ||||   ||   |||| |  |  ||  |  |||  | |  || |||  ||   |||| |||| || || | | ||  |||||    |  ||  |  |                                     
GTAATGGCTGTTATGTCAATGTGGACCAGATTACAACCACTTTATGCTTCTAACATGTGGAATGAGGCCCTTAATAAACGACTTGGGACTGAGgtatgtacagactta---taa--cattcttgtagatactagtatgttacacttactattgattcaagc-ttatgcagagatcatta--taaaaataaaaagactacag-------------------------------------

upper sequence: GRMZM2G445478_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G04400.1 (Glycine max), 5'ss of exon 5

GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatatgc-ttagtttagttcattttcatccatttttttatctgctgtttctacgacggaagcattattcaaggtgactaattaaaagctcatcgatcagtggctgaggataccatggcatgcttttgcttggatgtag
|||||  |  | ||||| |||||||| ||| |||||||    |||||| | ||||||||||| ||||| || ||||||||  | ||||||||||||| | |     || || ||     |     | | |   |  || | ||||  ||| |||       ||| ||    ||  ||||    |  ||| || |||      |                                 
GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCGCTGAACAAGCGGTTAGGGACTGAGgtatatcttgatgttggtcta--cagtagatgtgcttacatgaatatactgtc-ctatgactt--cttttactctttatgtgtaat----atttca-cggtcaaaacaag---------------------------------

upper sequence: GRMZM2G445478_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G03160.1 (Glycine max), 5'ss of exon 5

GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatatgc-ttagtttagttcattttcatccatttttttatctgctgtttctacgacggaagcattattcaaggtgactaattaaaagctcatcgatcagtggctgaggataccatggcatgcttttgcttggatgtag
|||||  |  | ||||| |||||||| ||| |||||||    |||||| | ||||||||||| |||||||| ||||||||  | ||||||||||||| | |     || || ||    ||   ||| | |   |  || |  |||  ||| ||        |  || |   |   |   ||| |  ||| |  |||   ||  ||                               
GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttgatgttggtcta--caatagacatgcttacatgaatatattgtc-ctatgatt------tcttttactttttatgggtaacatttca-cagtca--agccaag-------------------------------

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|78118584|gb|DV536968.1|DV536968

EST:     ATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG                         AAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC
genomic: ATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatat ... ttggatgtagAAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC

EST: gi|149100003|gb|EE186056.2|EE186056

EST:     ATGCTTCCCACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG                         AAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC
genomic: ATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatat ... ttggatgtagAAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC

EST: gi|78118583|gb|DV536967.1|DV536967

EST:     ATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG                         AAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC
genomic: ATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatat ... ttggatgtagAAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC

EST: gi|149015788|gb|EE045483.2|EE045483

EST:     ATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG                         AAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC
genomic: ATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatat ... ttggatgtagAAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC

EST: gi|76931485|gb|DV172738.1|DV172738

EST:     ATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG                         AAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC
genomic: ATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatat ... ttggatgtagAAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCC

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: 36 (upstream exon), 45 (downstream exon)
Score: 15

GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatat ... ttggatgtagAAACTGGACCTCCATGGGATCATTAGGGAGACCGAGAGACGGGGCCTGTCCTTCAACCAGCTGCTCACCGTACCTGAGCGAGACGACTGGGAGTACAGCG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 38

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 19