ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTCAATTTTGGTCTTCCTCCCTGTTACCGTTTATTCTCTAATTAGAGGATCTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTTgtaagtaaatccctcacaattgactgttttacaacatgtatgagtttgactgatcatgacaagtttatgctag

Basic information

species	Zea mays
transcript	GRMZM2G051262_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G051262_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g11070.1 (Oryza sativa), 5'ss of exon 4

CTCAATTTTGGTCTTCCTCCCTGTTACCGTTTATTCTCTAATTAGAGGATCTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTTgtaagtaaatccctcacaat-tgactgtttt-acaac-atgtatgagtttga-ctgatcatgacaagtttatgctag
|||||||||||| || |||||| |||| ||||| || ||||||||||||||||| ||||| || ||| ||||||||||| |||||||  ||| | |||||||||||    |    | | | | | |||||| ||||  | ||   | ||||| |||||  ||| |  |  |||| ||
CTCAATTTTGGTGTTTCTCCCTATTACGGTTTACTCACTAATTAGAGGATCTTTCAGAAGAGTATTTTTATCTGGATTTCTGACTTCCATGTTCCTTCTTgtaagttgcacatgtatattgtcattgtttttacaatgaagtccaaatttgatctgattgtgaaagttgcatgccag

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|26455879|gb|CA827462.1|CA827462

EST:     CTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTT                         GTTCTTTCGTTTGTTGCTGATTATTACTGCTATGGTCGATTGACATTCTCG
genomic: CTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTTgtaagtaaat ... tttatgctagGTTCTTTCGTTTGTTGCTGATTATTACTGCTATGGTCGATTGACATTCTCG

EST: gi|19822128|gb|BQ048152.1|BQ048152

EST:     ATTTGTGACTTCACTGTGCTTTCTT                         GTTCTTTCGTTTGTTGCTGATTATTACTGCTATGGTCGA-TGACATTCTCG
genomic: ATTTGTGACTTCACTGTGCTTTCTTgtaagtaaat ... tttatgctagGTTCTTTCGTTTGTTGCTGATTATTACTGCTATGGTCGATTGACATTCTCG

EST: gi|19822043|gb|BQ048067.1|BQ048067

EST:     CTATCTGGATTTGTGACTTCACTGTGCTTTCTT                         GTTCTTTCGTTTGTTGCTGATTATTACTGCTATGGTCGATTGACATTCTCG
genomic: CTATCTGGATTTGTGACTTCACTGTGCTTTCTTgtaagtaaat ... tttatgctagGTTCTTTCGTTTGTTGCTGATTATTACTGCTATGGTCGATTGACATTCTCG

EST: gi|74233286|gb|DT641200.1|DT641200

EST:     CTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTT                         GTTCTTTCGTTTTGT-GCTGATTATTACTGCTATGGTCGATTGACATTCTC
genomic: CTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTTgtaagtaaat ... tttatgctagGTTCTTTCGTTT-GTTGCTGATTATTACTGCTATGGTCGATTGACATTCTC

EST: gi|71772097|gb|DR970034.1|DR970034

EST:     CTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTT                         GTTCTTTCGTTTGTTGCTGATTATTACT
genomic: CTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTTgtaagtaaat ... tttatgctagGTTCTTTCGTTTGTTGCTGATTATTACT

EST: gi|149100385|gb|EE186457.2|EE186457

EST:     CTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTT                         GTTCTTTCGTTTGTTGCTGATTATTACTG
genomic: CTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTTgtaagtaaat ... tttatgctagGTTCTTTCGTTTGTTGCTGATTATTACTG

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), 43 (downstream exon)
Score: 97

CTCAATTTTGGTCTTCCTCCCTGTTACCGTTTATTCTCTAATTAGAGGATCTTTTAGAAGGGTTTTTCTATCTGGATTTGTGACTTCACTGTGCTTTCTTgtaagtaaat ... tttatgctagGTTCTTTCGTTTGTTGCTGATTATTACTGCTATGGTCGATTGACATTCTCGGTGTTCAATCTTCTGAAATATAACGTTATTGGTGGCGGCGAAAGTCACT

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 37

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54