ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGCCCCTTATTTGGTTGGACTGGTTGTACAGTTTGCATTTGAACAGTATGCACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgttcttaatttgtattggtatgattgtgttatgaccggaataacatacaggcgcagagataagaagagttagttagagagatagcagatctc...

Basic information

species	Zea mays
transcript	GRMZM2G034975_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G034975_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g50830.1 (Oryza sativa), 5'ss of exon 4

TGCCCCTTATTTGGTTGGACTGGTTGTACAGTTTGCATTTGAACAGTATGCACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgttctta-atttgtattggtatgattgtgttatgaccggaataacatacaggcgcagagataagaagagttagttagagagatagcagatctc
|||||||||| ||||||| || |||||||| || ||||| || |||||||||||||||||||||||||||||||||||||| || ||||| ||||| |||||||  | || |||| |||| |  ||||   ||||  |  |||    ||      |        |   |    | | | |  |    |       ||| | 
TGCCCCTTATCTGGTTGGTCTTGTTGTACAATTCGCATTCGAGCAGTATGCACGGCATCGGAAATCACCTTCTTGGCCAGTTATCCCTATCATCTTTAAGgtaacctggtgcttatatttatcctggtgctattggatcctgaaacaaaagcttaatccattgtgctttccttataatcaagtgtgcactggtgtgattt-

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|76010384|gb|DT937554.1|DT937554

EST:     CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAG                         GTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

EST: gi|6021699|gb|AW066627.1|AW066627

EST:     CCCGGCATCGGAAATCCCCTTCTTGGCCAGTGATTCCTATTATTTTCAAG                         GTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

EST: gi|113830349|gb|DW945549.1|DW945549

EST:     CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAG                         GTATACAGGCTACACCAACTGAACAGGGCAGCTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTC

EST: gi|76933225|gb|DV173376.1|DV173376

EST:     CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAG                         GTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

EST: gi|211380705|gb|FK985997.1|FK985997

EST:     CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAG                         GTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

EST: gi|78024486|gb|DV492873.1|DV492873

EST:     CACGGCATCGGAAATCACCTTCTGGGCCAGTGATTCTTATTATCTTCAAG                         GTATACAGGTTACACCAACTGAACAGGGCAGTTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

EST: gi|71326146|gb|DR799759.1|DR799759

EST:     CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAG                         GTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

EST: gi|76910323|gb|DV163807.1|DV163807

EST:     CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAG                         GTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

EST: gi|211280260|gb|FL478200.1|FL478200

EST:     CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAG                         GTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

EST: gi|50332228|gb|CO527354.1|CO527354

EST:     CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAG                         GTATCCAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

EST: gi|78079426|gb|DV507838.1|DV507838

EST:     CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAG                         GTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC
genomic: CACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTC

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: 46 (upstream exon), 46 (downstream exon)
Score: 16

TGCCCCTTATTTGGTTGGACTGGTTGTACAGTTTGCATTTGAACAGTATGCACGGCATCGGAAATCACCTTCTTGGCCAGTGATTCCTATTATCTTCAAGgtaattttgt ... ctcctttcagGTATACAGGCTACACCAACTGAACAGGGCAGCTCAGCTGGTGACGGCACTCACATTTTCTGTCAGAGGAACAGAGACAACAAATCAAACCCTAGCCATCA

Block sizes: 39 (upstream exon), 42 (downstream exon)
Score: 25

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 11