ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGCTGTAGAGCAAAATCCTGCCCAAGGATTGAATGCTAATCAAAGTCCAGCTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgtactcttattttctttctcaggctgtatgctagttgaactattgtgctggtaaatttttataggggcatgttctcttctactgacacctgtgaaatgaattctgctttatacag

Basic information

species	Zea mays
transcript	GRMZM2G137236_T01
intron #	19
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 19

TGCTGTAGAGCAAAATCCTGCCCAAGGATTGAATGCTAATCAAAGTCCAGCTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgtactcttattttctttctcaggctgtatgctagttgaactattgtgctggtaaatttttataggggcatgttctcttctactgacacctgtgaaatgaattctgctttatacag
||||||||| ||||| ||||  |||||| || |  ||||||||||||||| |||||| |||||||| || |||||||| |||||||| ||||||||||||||||  |||||||          ||||||     | || |       ||| | |  |  ||  ||| || |  || ||| | | ||||    ||                || | || |||||
TGCTGTAGAACAAAACCCTGTTCAAGGACTGGAGACTAATCAAAGTCCAGTTGGTGATTTGGCACTAGCAACCCTTGAAGATCAGTCAAACTCAGTTCAGgtacatgtgtact----------ttctcatagcatttgttcccccttctaattttattttat-tttatacaatggaatgatatattctgactac---------------cctaccttgtacag

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|211363573|gb|FL059329.1|FL059329

EST:     TGGTGACTTGGCACTTGCTACCCTTGATGATCAGGTCCAACTCAGTTCAG                         CCAATTGTCAACGTTCCGAAGGAGAAGTTTTCATATTTTGTGCAC
genomic: TGGTGACTTGGCACTTGCTACCCTTGATGATCAG-TCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGT-C-GA-GGAGAAGTTT-CATATTTTGTGCAC

EST: gi|71439223|gb|DR820273.1|DR820273

EST:     CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
genomic: CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT

EST: gi|211363570|gb|FL059326.1|FL059326

EST:     TTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
genomic: CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT

EST: gi|40336758|gb|CK370828.1|CK370828

EST:     CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
genomic: CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT

EST: gi|38502665|gb|CF972525.1|CF972525

EST:     CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
genomic: CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT

EST: gi|211363572|gb|FL059328.1|FL059328

EST:     TGGTGACTTGGCACTTGCTACCCTTGATGATCAGGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCCGAGGAGAAGTTTCATATTTTGTGCACAAA
genomic: TGGTGACTTGGCACTTGCTACCCTTGATGATCAG-TCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTC-GAGGAGAAGTTTCATATTTTGTGCACAAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 97

TGCTGTAGAGCAAAATCCTGCCCAAGGATTGAATGCTAATCAAAGTCCAGCTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGTGGGGTGCTGTACGAGGATCCTTACATCCAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122