ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACAAGAAGAGCGGAGTTCCATGGTTCTGGATTGATTGGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAGgtttgcctcttcctaatttgcgtgacaaatggtagtctattaataaatgatgcactcttgagcttgacttcttaattgtctttctttag

Basic information

species	Zea mays
transcript	GRMZM2G161299_T04
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G161299_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g13300.2 (Oryza sativa), 5'ss of exon 2

ACAAGAAGAGCGGAGTTCCATGGTTCTGGATTGATTGGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAGgtttgcctcttcctaatttgcgtgacaaatggtagtctattaataaatgatgcactcttgagcttgacttcttaattgtctttctttag
|| |||||||| || ||||||||||||||||| |||||||| || |||||||||| ||| |||||||| |||||||||||||||||||| | || | |||  |||||       ||  |        ||| |    |||||| |||||||||||||   |||   ||| | ||||
ACTAGAAGAGCAGAATTCCATGGTTCTGGATTAATTGGATCATTTCGAACAATCTCTCGAACAGAAGGGCTTTTAGGGTTTTACAGgttggtct-tgcctgctttgctacttgcataatg-------aatgacaattgcactgttgagcttgactttggaat---cttcccttag

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|76294060|gb|DV033628.1|DV033628

EST:     GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAG                         GGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTATGCAGCTTTGCATTA
genomic: GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAGgtttgcctct ... ctttctttagGGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTATGCAGCTTTGCATTA

EST: gi|211359789|gb|FL457496.1|FL457496

EST:     GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAG                         GGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTA
genomic: GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAGgtttgcctct ... ctttctttagGGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTA

EST: gi|211538575|gb|FL022784.1|FL022784

EST:     GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTYTTAGGGTTTTACAG                         GGGAAATGGAGC
genomic: GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAGgtttgcctct ... ctttctttagGGGAAATGGAGC

EST: gi|38687749|gb|CK144780.1|CK144780

EST:     GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAG                         GGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTATGCAGCTTTGCATTA
genomic: GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAGgtttgcctct ... ctttctttagGGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTATGCAGCTTTGCATTA

EST: gi|211538580|gb|FL022789.1|FL022789

EST:     GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAG                         GGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTATGCAGCTTTGCATTA
genomic: GGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAGgtttgcctct ... ctttctttagGGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTATGCAGCTTTGCATTA

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), 43 (downstream exon)
Score: 65

ACAAGAAGAGCGGAGTTCCATGGTTCTGGATTGATTGGATCCTTCCGAACAATCTATCGGACAGAAGGTCTTTTAGGGTTTTACAGgtttgcctct ... ctttctttagGGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTATGCAGCTTTGCATTATATGGCCTATGAAGAATACCGCCGGTGGATCATTCTTGGCTTTCCTAAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147