ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCACGCCGTATGTGCTCCTGCGGCGCCCCGACGGAGGCGTCTTCACCGACGACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtccattccgagcctcttttatttcgtcagtcacaatcaggacaatttatagtcaaccaagcatggtttcatccattcgagttgctatttgga...

Basic information

species	Zea mays
transcript	GRMZM2G124051_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G124051_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g07080.3 (Oryza sativa), 5'ss of exon 2

TCACGCCGTATGTGCTCCTGCGGCGCCCCGACGGAGGCGTCTTCACCGACGACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagc-agtccat-tccgagcct-cttttatttcgtcagtcacaatc--aggacaatttatagtcaaccaagcatggtttcatccattcgagttgctatttgga
||||||| || |||||||||||||||||||| || ||| ||| |||||| || |||  |||| ||   ||  |||||||| |||| ||||| || || |||||||  ||  ||  || || ||| |   |  |||     ||  | ||       ||| | || | ||   |   ||       | ||  || | | | |     
TCACGCCCTACGTGCTCCTGCGGCGCCCCGATGGCGGCATCTCCACCGAAGATGTGCATGAGGCCATCCCTCTGGATGGGCACTTTATGCGGTATAAATGgtgagttagctcacatctgaaccttcaaatgattcaaatttcctagtcttgtagaaatgtttacttaattgaagttgcaaatgactata-gattcgtttta----

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|71429759|gb|DR810809.1|DR810809

EST:     GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         GTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC
genomic: GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|149039469|gb|EE046609.2|EE046609

EST:     GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         GTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC
genomic: GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|211532376|gb|FL244241.1|FL244241

EST:     GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         GTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCGAC
genomic: GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|211532377|gb|FL244242.1|FL244242

EST:     GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         GTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCCAC
genomic: GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|148947123|gb|EC892433.2|EC892433

EST:     GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         GTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC
genomic: GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|211532380|gb|FL244245.1|FL244245

EST:     ACGTGTCTGAGAC-GCGNCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         G-ACCGCATACNAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC
genomic: ACGTGTCTGAGACCGCG-CCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|211532373|gb|FL244238.1|FL244238

EST:     ACGTGTCTGAGACCG-GNCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         GTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC
genomic: ACGTGTCTGAGACCGCG-CCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|211532371|gb|FL244236.1|FL244236

EST:     GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         GTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC
genomic: GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|149078953|gb|EE167793.2|EE167793

EST:     GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         GTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGGACACCCAAC
genomic: GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|149082745|gb|EE171964.2|EE171964

EST:     GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTG                         GTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC
genomic: GACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAAC

EST: gi|211532375|gb|FL244240.1|FL244240

EST:     GTGTCTGAGACCGCGCCNNCGTGGATGGGTACTTCATGGCGCTACAAGTG                         GTACCGCNATACAAAGTGANTCGTAGAGCTGCTAATCTGCAGTGTACACCC
genomic: GTGTCTGAGACCGCGCC--CGTGGATGGGTACTTCATG-CGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGC-ATACAAAGTGA-TCGTAGAGCTGCTA-TCTGCAGTGTACACCC

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: 44 (upstream exon), 49 (downstream exon)
Score: 80

TCACGCCGTATGTGCTCCTGCGGCGCCCCGACGGAGGCGTCTTCACCGACGACGTGTCTGAGACCGCGCCCGTGGATGGGTACTTCATGCGCTACAAGTGgtgagcagtc ... tttcttgaagGTACCGCATACAAAGTGATCGTAGAGCTGCTATCTGCAGTGTACACCCAACAGAACAAGCAACACTTCAGTGCATAGGGTGTCTGAAGTCAAAAATACCT

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 54

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68