ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAAGCCTCTGTTCGTGATCCCCCATGACAAGCACAGAGAGGAGGTCGAGGAGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggttgtctcatctgttctagtacatgataatctccatacgctgcagaatggaaatggtacctctgaatctgaaagatggcttaccatgccattttctgaccgactcccaag

Basic information

species	Zea mays
transcript	GRMZM5G838196_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G838196_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g17390.1 (Oryza sativa), 5'ss of exon 4

CAAGCCTCTGTTCGTGATCCCCCATGACAAGCACAGAGAGGAGGTCGAGGAGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcg----gttgtctcatctgttctagtacatgataatctccatacgctgcagaatggaaatggtacctctgaatctgaaagatggcttaccatgccattttctgaccgactcccaag-----
 ||||||||||| |||||||| ||| | |||||||| || ||||| ||||||   |||||| | ||||| || ||||||||||||||||| || || || |||||      | ||  || ||  | | |  || |   |||||  | || |   |||       |   |  |    ||   ||   |   ||||   |   ||||||    |    ||| |     
GAAGCCTCTGTTTGTGATCCCTCATCAGAAGCACAGGGAAGAGGTTGAGGAGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctttgatgcttcttcattacaatcactttgcaatctgaaaacaccttagatcatctttcacaggta-acattacaattctttattactgagt-gttttctttttgtgatccatgataag

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|211467385|gb|FL438566.1|FL438566

EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT

EST: gi|148962266|gb|EE013089.2|EE013089

EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGGGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT

EST: gi|13557980|gb|BG549336.1|BG549336

EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT

EST: gi|211164012|gb|FL463865.1|FL463865

EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT

EST: gi|211164011|gb|FL463864.1|FL463864

EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT

EST: gi|211467384|gb|FL438565.1|FL438565

EST:     AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT
genomic: AGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCT

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 2 RNA-Seq libraries.

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 29

CAAGCCTCTGTTCGTGATCCCCCATGACAAGCACAGAGAGGAGGTCGAGGAGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcggtt ... gactcccaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG