ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCTGAGTACAATGCCATCTCATATTCTGACCAAATGAGATTAAGAACAGCAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattgcttgcacttttgctcatggatctggatctctctgttttgtatcgtttaaacatgttctggatgcaagtcatgagaccactgcgtttttgtttggtatgtacattccttctcgttgaagtacctaacacaaaaacacttttatgatattcctatatag

Basic information

species	Zea mays
transcript	GRMZM2G085438_T03
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G085438_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g49380.1 (Oryza sativa), 5'ss of exon 7

GCTGAGTACAATGCCATCTCATATTCTGACCAAATGAGATTAAGAACAGCAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattgcttgcacttttgctcatggatctg--gatctctctgttttgtatcgtttaaacatgttctggatgcaagtcatgagaccactgcgtttttgtttggtatgtacattccttctcgttgaagtacctaacacaaaaacacttttatgatattcctatatag
||||||||||||||||| |||||| |  | |||||||| || || ||||||||||||||||| || || || |||||||| ||||| |||||||| ||||||| | ||||||  || ||  ||  |  | | |  ||  || || || |  ||  || |    ||  ||||| ||||    ||  | |||| |  |||||     ||  ||||                ||| | |||                              
GCTGAGTACAATGCCATTTCATATACCCAACAAATGAGGTTGAGGACAGCAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAGgtcagtgttgcttttaccttatctttttaagcggttgaattcccttttctaaattattcag---tgc-ctggaagcaaccattgccatcacttc--ttttgaaaaatagttacaaatgcgaaaccctctttacttgacag-----------------------------

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|71759858|gb|DR957795.1|DR957795

EST:     CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAG                         ATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT
genomic: CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT

EST: gi|78123598|gb|DV541982.1|DV541982

EST:     CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAG                         ATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT
genomic: CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT

EST: gi|110518313|gb|EE022900.1|EE022900

EST:     CAGTTGAACTTTTAAAAGCCACGAAGGACATGGAATCACAGTTGGAAAAG                         ATCTCCTCTCCATTGCGGATTCTTCACGGAGCCGCAGACATGGTAACCGAT
genomic: CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT

EST: gi|78082085|gb|DV510497.1|DV510497

EST:     CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAG                         ATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT
genomic: CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT

EST: gi|40333901|gb|CK367971.1|CK367971

EST:     CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAG                         ATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT
genomic: CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT

EST: gi|110523789|gb|EE027973.1|EE027973

EST:     CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAG                         ATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT
genomic: CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT

EST: gi|86468691|gb|DY235061.1|DY235061

EST:     CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAG                         ATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT
genomic: CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT

EST: gi|71759897|gb|DR957834.1|DR957834

EST:     CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAG                         ATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT
genomic: CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT

EST: gi|37375743|gb|CF624330.1|CF624330

EST:     CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAG                         ATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT
genomic: CAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGAT

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: 41 (upstream exon), 48 (downstream exon)
Score: 18

GCTGAGTACAATGCCATCTCATATTCTGACCAAATGAGATTAAGAACAGCAGTTGAACTTTTAAAAGCCACGAAGGACATTGAATCACAGTTGGAAAAGgtcactattg ... tcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGATCCTCAGGTCAGCAAATTCCTTTATGAGAAAGCCAGCACGAAGGACAAGA

Block sizes: 41 (upstream exon), 33 (downstream exon)
Score: 15

Block sizes: 35 (upstream exon), 48 (downstream exon)
Score: 18