ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gttggtccttaattatcattttcttatcctagatatctctattaattatataagtgaatcctttgttcttatgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATATGGTGCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACA

Basic information

species	Zea mays
transcript	GRMZM2G088974_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G088974_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g08270.1 (Oryza sativa), 3'ss of exon 6

gttggtccttaattatcattttcttatcctagatat--ctctattaattatataagtgaatcctttgttcttatg-taattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATATGGTGCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACA
||||||||  ||   |    | | ||   |   | |      | |||| | | |||| ||||   |  | ||||| |    ||||||||||| | | ||||||||| |||||||| |||||||||||||||||||||||  |||| |  |||||||| ||||||| |  |||  | || ||||
gttggtccccaaaagttgcatacctaatttgtttctgatatgaataatcacacaagtaaatctgattatattatgcttggcagAAACTTGGTATTCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATATGGTGCTGTAGCCCAAGGTGATGGCGCCATTTATTGGCGATTTCCACACA

upper sequence: GRMZM2G088974_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 6

-------------------------gttggtccttaattat-cattttctta---tcctagatatctctatta-attatataagtgaat---------cctttgttcttatgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATATGGTGCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACA
                          ||  |||||| | ||  ||||| |||   |   |  || |||| ||| |||  ||  |   |          || || ||  |   | |  ||||||||||||||  ||| || || || ||||| |||||||||||||||||||| ||  |  || | || ||||| || || | | ||||  |||| ||||
gtagtactgtttctatagttaacacatttttccttattcatatatttttttagtttttcatttagctcttttagatttaatctgcagacatttcttgaccattattacttcatgaacagAAACTTGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA

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|37375807|gb|CF624370.1|CF624370

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|76013309|gb|DT940479.1|DT940479

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTC
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTC

EST: gi|32933227|gb|CF038039.1|CF038039

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|60672399|gb|DN475149.1|DN475149

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|32928793|gb|CF033605.1|CF033605

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|113702970|gb|EE680474.1|EE680474

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|101401650|gb|EB822490.1|EB822490

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|5006217|gb|AI712279.1|AI712279

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|71762698|gb|DR960635.1|DR960635

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|88753523|gb|DY537664.1|DY537664

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|50334940|gb|CO530066.1|CO530066

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|9952566|gb|BE639254.1|BE639254

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|32929425|gb|CF034237.1|CF034237

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|89754586|gb|DY685314.1|DY685314

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|86467594|gb|DY233964.1|DY233964

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|50334941|gb|CO530067.1|CO530067

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|6465587|gb|AW191182.1|AW191182

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|211320348|gb|FL456168.1|FL456168

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|93011705|gb|EB637225.1|EB637225

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|9731309|gb|BE510061.1|BE510061

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|71766942|gb|DR964879.1|DR964879

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|40333919|gb|CK367989.1|CK367989

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|44901269|gb|CK827814.1|CK827814

EST:     AAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: AAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|149080860|gb|EE169940.2|EE169940

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|76013308|gb|DT940478.1|DT940478

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|60338966|gb|DN205939.1|DN205939

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|32929156|gb|CF033968.1|CF033968

EST:     AGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: AGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

EST: gi|78075089|gb|DV503523.1|DV503523

EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

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: 143

ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATATGGTGCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 60

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atcctagatatctctattaattatataagtgaatcctttgttcttatgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATATGGTGCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACA