ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACATCCAACAGAAAAGAGGGACTTGTACAACCCAGATCACGGGAAGAAGGTCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgattcacatacatttccatgtgacattgtcctattcattgaaatgtccagcagtcaccgcatgtggatgcacattttgagcggtcacagtaccc...

Basic information

species	Zea mays
transcript	GRMZM2G158147_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158147_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g02050.1 (Oryza sativa), 5'ss of exon 3

ACATCCAACAGAAAAGAGGGACTTGTACAACCCAGATCACGGGAAGAAGGTCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgattcacata-----catttccatgtgac--attgtcctattcattgaaatgtccagcagtcaccgcatgtggatgcacattttgagcggtcacagtaccc-------
 ||||||||||||||||||||  |||||||||||||||| || ||||||||||| |||||||| || ||||||||||||||||||||| |||||||||||||||||||| |||| |     ||||  ||| | |   ||| || | |   ||||     |  | | | |||  || |   | |      | |      | | ||          
CCATCCAACAGAAAAGAGGGATCTGTACAACCCAGATCATGGAAAGAAGGTCCTTAGCATGGCCCCAGGTTTAGAGAAACTCAACATATTGCCCTTCAAGgtatttgatgcacagaaaaagcattagcatttaatgaattatcatttgttttgaggaaacatgtaat-accagatttttgttctttccctaaaaataaatactatttgctccag

upper sequence: GRMZM2G158147_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5

ACATCCAACAGAAAAGAGGGACTTGTACAACCCAGATCACGGGAAGAAGGTCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtattt---gattcacatacatttcc------atgtgacattgtcctattcattgaaatgtccagc-agtcaccgcatgtggatgcacattttgagcggtcacagtaccc
 || || || |    | | ||  | ||| || |||| ||||| |||| ||| || ||||||||||||||  | ||||| |||||||| |||||||||| |||| ||   || | |||  |  |  |      ||||  |  |||| | |   |||   |||    | | ||| | ||| || |  || || |  ||   |          
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccagaatgacagcccctatctgataaatgtttctctgtcgtttatgttgtgctgtgagactactcagctcatctgaa-acaaatgtgtagaaatg---------

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|60338703|gb|DN205676.1|DN205676

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAA

EST: gi|211399264|gb|FL448232.1|FL448232

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32830226|gb|CD969904.1|CD969904

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32828661|gb|CD968339.1|CD968339

EST:     TCCTGAGCATGGCTGGTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|78180099|gb|DV550472.1|DV550472

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32829799|gb|CD969477.1|CD969477

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32829244|gb|CD968922.1|CD968922

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32828636|gb|CD968314.1|CD968314

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32830289|gb|CD969967.1|CD969967

EST:     CTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: CTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|60346069|gb|DN213042.1|DN213042

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32830236|gb|CD969914.1|CD969914

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|60357884|gb|DN224857.1|DN224857

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|32829367|gb|CD969045.1|CD969045

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

EST: gi|148942989|gb|EC888037.2|EC888037

EST:     TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAG                         GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA
genomic: TCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCA

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: 38

ACATCCAACAGAAAAGAGGGACTTGTACAACCCAGATCACGGGAAGAAGGTCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtatttgatt ... cctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 87

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