ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGCTGGAATAGCAAGGCATGGAGTTGGAAAATGGCGCACAATATTGAAAGATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatattttcactttattcttcttacctgatcttgttttagtgtatgtcatttcaaactttctgtttgttaaaatttttatgagtcatttgtaaatttccacatgttatctttggtcttagtgtgcattcttcaattatgctaattaatacttag

Basic information

species	Zea mays
transcript	GRMZM2G095239_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G095239_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G03390.2 (Glycine max), 5'ss of exon 2

AGCTGGAATAGCAAGGCATGGAGTTGGAAAATGGCGCACAATATTGAAAGATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatattttcactttattcttcttacctgatcttgttttagtgtatgtcatttcaaactttctgtttgttaaaatttttatgagtcatttgtaaatttccacatgttatctttggtc-ttagtgtgcattcttcaattatgctaattaatacttag
||| ||| | |  | |||||| ||||| ||||||||||| ||| |||| |||||||| ||||||     ||| | |   || |||||||| |||||||||||  | |      || || ||  |   |  || |  ||||||| | | |     ||||   ||||  |||  | | ||| | |||| | | | ||   |      || |||   |       | || |   |  |||   ||||    ||   |  |||
AGCCGGAGTTGTCAAGCATGGTGTTGGTAAATGGCGCACCATACTGAAGGATCCAGAGTTTAGTAGTGTCTTGTACCTGCGGTCAAATGTGGATCTCAAGgtctggt-----taccttgttggttgcatttgttgatgttttattttgttgaggttcattatttcattttccttacattgtaatgaattagt-gttggtccatctatattactatgcacaacttgtttttgtggttctgatatggggttttgga--tag

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|89761715|gb|DY689620.1|DY689620

EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC

EST: gi|211130407|gb|FL313028.1|FL313028

EST:     GCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: GCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC

EST: gi|76287133|gb|DV026701.1|DV026701

EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC

EST: gi|78105940|gb|DV524358.1|DV524358

EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATG
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATG

EST: gi|50329506|gb|CO524632.1|CO524632

EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC

EST: gi|74244193|gb|DT652107.1|DT652107

EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC

EST: gi|60359172|gb|DN226145.1|DN226145

EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGAC

EST: gi|76280710|gb|DV020278.1|DV020278

EST:     ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAG                         GACAAGTGGCGAAACATGAATGTGATTGTCAGTACATC
genomic: ATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATC

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: 94

AGCTGGAATAGCAAGGCATGGAGTTGGAAAATGGCGCACAATATTGAAAGATCCAGAATTTAGTTCCACCTTATGCTACCGCTCAAATGTTGATCTCAAGgttcgatatt ... taatacttagGACAAGTGGCGAAACATGAATGTGATTGTCAGTACATCGAGTTCTCGTGACAAGGCGAAGTCTGCATTGAAGAGAATACGAACTATTCCCAAGAATAATG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 69