ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactgcttttcaagtttgaacagatttgaatcttgtatgtttgataccttcattcacttcaatattgtcatacag

Basic information

species	Zea mays
transcript	GRMZM2G023020_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G023020_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g32670.1 (Oryza sativa), 5'ss of exon 3

CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactgcttttcaagtttgaacagatttgaat-------cttgtatgtttgataccttcattcacttcaatattgtcatacag
||||||||||  |||| ||||||||||| ||||||||||| |||||||||||||| || |||||||| || |||||||||||||| || |||||||||||||    | || |||| ||||   ||||||| |||||       ||| |   ||||   | |  | |||||||| |  ||| ||||||
CTCACTTGATCCCCCCTGACACTCCACGTTCAATCTTCGTCTACTTCCGGGGACTATTCTATGACACTGGAAATGACCCCGAGGGTGGTTACTATGCAAGgttagcaatgtttttaaagt---aacagatctgaatttttatccttctggttttgtcccatgtactcacttcagtgatgttatacag

upper sequence: GRMZM2G023020_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G37920.1 (Glycine max), 5'ss of exon 3

CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactgcttttcaagttt---gaacagatttgaatcttgtatgtttgatacctt-cattcacttcaatattgtcatacag-----------------
| ||| | ||| |   | | |||||  | || || || ||||||||||| ||||| ||||||||    || |||||||| || || |||||||||||||||||     |  || | |    |    ||   |   ||    || |  | |||  | || |||| | ||    |   |  |   |                 
CACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTCCGAGGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgtcttatttattacaactcacaaatgtaaaggaggggtggacatgtgaggcttttcatttatttttgcagcat-gtctggttaagaccactaacttg

upper sequence: GRMZM2G023020_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G17140.1 (Glycine max), 5'ss of exon 3

CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactgcttttcaagtttgaacagatttgaatct---tgtatgtttgatacctt-cattcacttcaatattgt-catacag----------------
| ||| | ||| |   | | |||||  | || || || |||||||| || ||||| ||||||||    || ||||||||||| || |||||||||||||||||     |  || | |      | || |||| ||      || || | |||  | || | || | ||    |   | | | |                  
CACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTTCGAGGACTGTTTTATGATGTTGGAAATGACCCCGAAGGTGGATACTATGCAAGgtatgtcttatttattacaaccca-caaatttaaagaggggtggatatgtgaggcttttcctttatttttgcagcatgcctgcttcagaccactaacttgc

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|40336812|gb|CK370882.1|CK370882

EST:     GGACTTTTTTATGACACGGGGAATGACCCTGAGGGCGGATACTACGCAAG                         AGGTGCGCGAGCTTCTTTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA

EST: gi|74237462|gb|DT645376.1|DT645376

EST:     GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA

EST: gi|88752698|gb|DY536839.1|DY536839

EST:     CCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: CCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA

EST: gi|76292971|gb|DV032539.1|DV032539

EST:     GACACGGGGAATGACCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA

EST: gi|78179883|gb|DV550256.1|DV550256

EST:     GGACTTTTTTATGACACGGGGAATGACCCTGAGGGCGGATACTACGCAAG                         AGGTGCGCGAGCTTCTTTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA

EST: gi|78117432|gb|DV535819.1|DV535819

EST:     CCCGAGGGCGGATTTTATGCAAG                         AGGTGCGGGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: CCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA

EST: gi|61118962|gb|DN559923.1|DN559923

EST:     GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA

EST: gi|74232586|gb|DT640500.1|DT640500

EST:     GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA

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), 49 (downstream exon)
Score: 106

CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 135

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