ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGAATCCTTGGATAGCAAGGGGAGAGTAATGGTGGAAAAGGATTTAAGAGTGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagtttttcactcccaacttgtaattctccttctgctttgtttattatgttactttattcaggttggtttttctcattgtcccaaccaccattcatta...

Basic information

species	Zea mays
transcript	GRMZM2G166145_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G166145_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g05680.2 (Oryza sativa), 5'ss of exon 2

GGAATCCTTGGATAGCAAGGGGAGAGTAATGGTGGAAAAGGATTTAAGAGTGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagtttttcactcccaacttgta-attctcct-tctgctttgtttatt-atgttactttattcaggttggtttttctcattgtcc-caaccaccattcatta
|||||||||||| | |||||| ||| ||||||||||||||||||||||| | ||||||| ||||||||||||||| |||||||||||||||||||||||||||||| |   |||   |||||| | |||||  | |  | | |  ||    ||||| | ||||||    || ||       || |   ||||    | |  || 
GGAATCCTTGGACAACAAGGGAAGACTAATGGTGGAAAAGGATTTAAGAATAAAAGGTTATAATAACATTTTTGCAATTGGTGACATCACAGATATTCCTgtaagtct---actttaaacttgcacattctgttattcgatctacttgcagatgttccattattccctctgtttgagaatgttctgtacaactgagagttctt-

upper sequence: GRMZM2G166145_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G09920.1 (Glycine max), 5'ss of exon 3

GGAATCCTTGGATAGCAAGGGGAGAGTAATGGTGGAAAAGGATTTAAGAGTGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagt--ttttcactcccaacttgtaattctccttctgctttgtttattatgttactttattcaggttggtttttctcattgtcccaaccaccattcatta
| |    ||||||      || ||  | | ||| ||     | || || ||    |||   |  ||||||||||| ||||| |||||||||||| |||| ||||||  || ||| |   | ||| |  |||  ||| |      | ||| || |||  |  ||          |     | |  || |     |    ||  
GAATGATTTGGATGATCTTGGAAGGATTAAGGTAGATGGAAAATTGAGGGTCGTTGGTAGGACAAACATTTTTGCAATTGGAGACATCACAGATGTTCCAgtaagtacttgtcattggtacctttttgttcagcttttcacaattatataattttatatgttttgtaacaaactcaacaagttaccaagttttctgctat--

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|71431204|gb|DR812254.1|DR812254

EST:     TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCT                         GAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG
genomic: TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG

EST: gi|86470823|gb|DY237193.1|DY237193

EST:     TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCT                         GAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG
genomic: TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG

EST: gi|89764194|gb|DY691090.1|DY691090

EST:     TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCT                         GAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG
genomic: TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG

EST: gi|5005950|gb|AI712012.1|AI712012

EST:     AACATTTTTGCGATTGGTGACATCACAGATATTCCT                         GAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGAGGCGAAG
genomic: AACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG

EST: gi|5650135|gb|AI920495.1|AI920495

EST:     TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCT                         GAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG
genomic: TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG

EST: gi|86470206|gb|DY236576.1|DY236576

EST:     TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCT                         GAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG
genomic: TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG

EST: gi|37377793|gb|CF625537.1|CF625537

EST:     TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCT                         GAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG
genomic: TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG

EST: gi|71431205|gb|DR812255.1|DR812255

EST:     TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCT                         GAAATCAAACAAAGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG
genomic: TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG

EST: gi|76915401|gb|DV165968.1|DV165968

EST:     TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCT                         GAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG
genomic: TGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAG

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), 47 (downstream exon)
Score: 55

GGAATCCTTGGATAGCAAGGGGAGAGTAATGGTGGAAAAGGATTTAAGAGTGAAAGGTTTTAATAACATTTTTGCGATTGGTGACATCACAGATATTCCTgtaagttttt ... cgctgttcagGAAATCAAACAAGGGTACCTCGCCCAGAAGCACGCGCTGCTAGTGGCGAAGAACCTGAAGCTACTGACCAAGGGTCTCCCTAACAGCAAACTGGCGACTT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 37

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 45