ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAACGCGTGCCCGCCGTACCTCGTCTACGTCGACGAGGCGCACAAGGAGATCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgccttccgttccgtcgtccagctcgcgagcaatcggcgatcggccgtcccgtcgtgagcgggagaggtttgacgggttgtcgctcgcgtcacgaattcctccgcag

Basic information

species	Zea mays
transcript	GRMZM2G174315_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G174315_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g14490.1 (Oryza sativa), 5'ss of exon 1

CAACGCGTGCCCGCCGTACCTCGTCTACGTCGACGAGGCGCACAAGGAGATCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgt-gcctgccttccgttccgtcgtccagctcgcgagcaatcggcgatcggccgtcccgtcgtgagcgggagaggtttgacgggttgtcgctcgcgtcacgaattcctccgcag
   | | ||||| || ||| |||||||||| ||| |    ||||||||| || |||||||| | |||||||||||||||   |||||||||||||||||||| | | ||   |  ||||     ||  | | ||| | | |  |||  |      || |     ||||      || ||  ||  | |   | || | |||   || | ||||
---CACCTGCCCTCCCTACATCGTCTACGTTGACCACCGCCACAAGGAGGTCGTCCTCGCCATCCGCGGCCTCAACCTCACCCGCAACGCCGACTACAAGGTCgtccgcaagcgattcc-----ccttcccccgatcgacc--cgaatg------ccatgaacggcggcgagatttggagagggaggctgactcggctcgatcccccctgcag

upper sequence: GRMZM2G174315_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g14490.2 (Oryza sativa), 5'ss of exon 1

CAACGCGTGCCCGCCGTACCTCGTCTACGTCGACGAGGCGCACAAGGAGATCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgt-gcctgccttccgttccgtcgtccagctcgcgagcaatcggcgatcggccgtcccgtcgtgagcgggagaggtttgacgggttgtcgctcgcgtcacgaattcctccgcag
|||| | ||||| || ||| |||||||||| ||| |    ||||||||| || |||||||| | |||||||||||||||   |||||||||||||||||||| | | ||   |  ||||     ||  | | ||| | | |  |||  |      || |     ||||      || ||  ||  | |   | || | |||   || | ||||
CAACACCTGCCCTCCCTACATCGTCTACGTTGACCACCGCCACAAGGAGGTCGTCCTCGCCATCCGCGGCCTCAACCTCACCCGCAACGCCGACTACAAGgtcgtccgcaagcgattcc-----ccttcccccgatcgacc--cgaatg------ccatgaacggcggcgagatttggagagggaggctgactcggctcgatcccccctgcag

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|78083301|gb|DV511694.1|DV511694

EST:     TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAG                         GTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG
genomic: TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgcct ... tcctccgcagGTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG

EST: gi|149095323|gb|EE180959.2|EE180959

EST:     TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAG                         GTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG
genomic: TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgcct ... tcctccgcagGTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG

EST: gi|71319200|gb|DR796355.1|DR796355

EST:     TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAG                         GTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG
genomic: TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgcct ... tcctccgcagGTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG

EST: gi|78077831|gb|DV506260.1|DV506260

EST:     TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAG                         GTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG
genomic: TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgcct ... tcctccgcagGTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG

EST: gi|50323331|gb|CO518457.1|CO518457

EST:     TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAG                         GTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG
genomic: TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgcct ... tcctccgcagGTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG

EST: gi|86466050|gb|DY232423.1|DY232423

EST:     TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAG                         GTGCTCTTGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG
genomic: TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgcct ... tcctccgcagGTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG

EST: gi|89247662|gb|DY619448.1|DY619448

EST:     TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAG                         GTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG
genomic: TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgcct ... tcctccgcagGTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG

EST: gi|88755924|gb|DY540065.1|DY540065

EST:     TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAG                         GTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG
genomic: TCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgcct ... tcctccgcagGTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTG

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: 28 (upstream exon), 44 (downstream exon)
Score: 2

CAACGCGTGCCCGCCGTACCTCGTCTACGTCGACGAGGCGCACAAGGAGATCATCCTCGCCGTGCGCGGCCTCAACCTCGTGCGCAACGCCGACTACAAGgtgcctgcct ... tcctccgcagGTGCTCATGGACAACAAGCTCGGGATGCAGATGTTCGACGGCGGCTACGTGCACCACGGCCTGCTCAAGGCCGCCAAGTTCATCCTGGAGCGGGAGACGG

Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 19

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 52