ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAAAGGACAACATTATTGGTGAGGGTGGATACGGTGTAGTTTATCGCGGGCAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttccttatctaatctcagctcgttatttacctgcttgtcttccttaccaatgttgcatttagtttctccaattgatgttttgtgaatctgtag

Basic information

species	Zea mays
transcript	GRMZM2G034855_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G034855_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g21960.1 (Oryza sativa), 5'ss of exon 2

CAAAGGACAACATTATTGGTGAGGGTGGATACGGTGTAGTTTATCGCGGGCAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttccttatctaatctcagctcg------ttatttac-ctgcttgtct-tccttaccaatgttgca------------tttagtttctccaattgatgttttgtgaatctgtag
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CAAAGGATAACATTCTTGGTGAGGGTGGATATGGTGTAGTTTATCGTGGCCAACTGATCAATGGCACTCCTGTTGCTGTTAAGAAGCTTCTCAATAACCTgtaagtcttgccctgcttatcagagtttgatctttttgtttattctccttgtctcttgtctccaataccacaaatcagacagctttaagtttttccaatcgatgttttgtaaacttgcag

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|87157535|gb|DY402324.1|DY402324

EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCT                         AGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGT
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGT

EST: gi|78074088|gb|DV502522.1|DV502522

EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCATTAACCT                         AGGTCAAGCTG
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTG

EST: gi|71416639|gb|DR803774.1|DR803774

EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCT                         ANGTCAAGCTGAGAAGGAAT
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAAT

EST: gi|22819564|gb|BU499654.1|BU499654

EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCT                         AGGTCAAGCTGAGAAGGAAT
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAAT

EST: gi|26559774|gb|CA832009.1|CA832009

EST:     CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCT                         AGGTCAAGCTGAGAAGGAATTTAGAGTA
genomic: CAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTA

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), 41 (downstream exon)
Score: 126

CAAAGGACAACATTATTGGTGAGGGTGGATACGGTGTAGTTTATCGCGGGCAGCTAATCAATGGCTCCCCTGTTGCTGTCAAAAAGCTTCTCAATAACCTgtaagccttc ... gaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 153

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 130