ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaattgaatatttttttcttcttgaagttaattcttaatcatcgacactatttgattcgaatgtactgttcttttcttctaag

Basic information

species	Zea mays
transcript	GRMZM2G132084_T03
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G132084_T04 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g46410.1 (Oryza sativa), 5'ss of exon 6

TGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaag-aaattgaatatttttttcttcttgaagttaattcttaatcatcgacactatttgattcgaatgtactgttctt-----ttcttctaag
| |||||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||| |||||||| ||||||||||||||||| |||||| ||||||||| || ||||  || |||   |||||| |   | |  ||  |||||     |||||| ||  ||  | ||| |  |     || || ||||
TAGTTGCAATAGCTTACACAATGTTGTCAGGGGAGGGTCAGTTCTACACATACATGGTTCTTATTTCAGAAACAACCACCCCTGAAATTAACTTGAGATGgtaagcaagttgagcatgtttcatttcttgtatgaagtcatt--tcatctcagttatttggttataacattctgatgctcggatttattttaag

upper sequence: GRMZM2G132084_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G45240.3 (Glycine max), 5'ss of exon 6

TGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaa----gaaattgaatattt-ttttcttcttgaagttaattcttaatcatcg-acactatttgattcgaatgtactgttcttttcttctaag
| || ||| || | |   |||||||| ||||||| || ||| | |||||||||||||| || || || |||||||| || ||||  ||||||||| ||||||||    | | || |||||    | | |   | | || | || || || |  | |||   | || ||   | |                    
TAGTAGCAGTATCATTTTCAATGTTGACTGGGGAGGGTCAGCTATACACATACATGGTCCTGATCTCTGAGACAACTACTCCTGGGATCAACTTGAGATGgtaatcttgcacttaaatatgcactctataggtcatgtaatttatttattaatgcacatattgtgtttgtgaag--------------------

upper sequence: GRMZM2G132084_T04 (Zea mays), 5'ss of exon 7
lower sequence: Vv12s0028g01000.t01 (Vitis vinifera), 5'ss of exon 5

TGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaa--attgaatatttttttcttcttgaagttaattcttaatcatcgacactatttgattcgaatgtactgttcttttcttctaag
| | |||| | || ||  |||||||| |||||||||||||  ||||||| ||||||||||| || || |||||||| ||||| |  ||||| ||| |||||||| |   |   ||||   |    |    |   ||| ||||      ||     | ||||||| | |  |   |||  |          
TAGCTGCAGTGGCATATGCAATGTTGACTGGGGAAGGGCAACTTTACACCTACATGGTTCTTATCTCTGAGACAACAACCCCAGGGATCAATTTGAGATGgtaacacccaactaataaaatgagttgacaggttttagttctgctctctc----ttttttgatttgcaacttgggtttgtaag-------

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|166452447|gb|EG305289.1|EG305289

EST:     AACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGC
genomic: -ACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaatt ... ttcttctaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGC

EST: gi|78076716|gb|DV505150.1|DV505150

EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaatt ... ttcttctaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG

EST: gi|211111684|gb|FL466622.1|FL466622

EST:     ATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: ATCAACTTGCGATGgtaagaaatt ... ttcttctaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG

EST: gi|166625864|gb|EG208558.1|EG208558

EST:     GAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTTACTTGGTTAATG
genomic: GAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaatt ... ttcttctaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTT-ACTTGGTTAATG

EST: gi|101387192|gb|EB815613.1|EB815613

EST:     ACATGGTTCTCATTTCAGAGACA-CCACCCCCTGAA-TCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTT
genomic: ACATGGTTCTCATTTCAGAGACAACCACCCC-TGAAATCAACTTGCGATGgtaagaaatt ... ttcttctaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 244

TGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaatt ... ttcttctaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 109

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 156