ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTCTAGCATGCCAAATGGACAACCAAAGTGGCTTCTTTGTTTCATACCAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTTgtaagttgccaacttcaaacccatctcagtacttggaaagaaaacagttccattcaacagtcataaaaaggatactcatttcattatctaataaatgcag

Basic information

species	Zea mays
transcript	GRMZM2G458538_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G458538_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 5'ss of exon 14

GTCTAGCATGCCAAATGGACAACCAAAGTGGCTTCTTTGTTTCATACCAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTTgtaagttgccaacttcaaacccatctcagtacttggaaagaaaacagttccattcaacagtcataaa----aaggatactcatttcattatctaataaatgcag
|||||||| ||||||||| || ||||| ||||| || | |||  |||||||||||||  ||||||||||||||||||||||||| ||||||||||||||||||           ||||   |             ||    || || ||||||| | | ||||      | | || | ||| ||| || ||   | |||||
GTCTAGCACGCCAAATGGGCAGCCAAAATGGCTCCTATCTTTTGTACCAGATTATCCATTGCTTAACTTCATGCTTACTACAGCAATCTATCTTCTTgtaagt----------gaacctgccc------------agggtgcattttcattcaaaaattataatcatcgaagttattaattccatgatgtat--actgcag

upper sequence: GRMZM2G458538_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G08730.1 (Glycine max), 5'ss of exon 15

GTCTAGCATGCCAAATGGACAACCAAAGTGGCTTCTTTGTTTCATACCAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTTgtaagttgccaacttcaaacccatctcagtacttggaaagaaaacagttccattcaacagtcataaaaaggat---actcatttcattatctaataaatgcag---------------------
||||| ||||||||| ||||| || ||||||||||||| | | || || || ||||||||||| ||||||||||| || || || || ||  |  |||||||   |    |||   |     |  ||   |       |   | |   ||||||   | || ||| | ||   ||| | ||     | | | |    | |                     
GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatcttctttccttctttcatttgtttatttttcttattaattaatattcaagtcttatgaaaggcatcatactaagttgcactttttacatgcactgctatcttgacatggtttgcag

upper sequence: GRMZM2G458538_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G25780.1 (Glycine max), 5'ss of exon 15

GTCTAGCATGCCAAATGGACAACCAAAGTGGCTTCTTTGTTTCATACCAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTTgtaagttgccaacttcaaacccatctcagtacttggaaagaaaacagttccattcaacagtcataaaaaggatactcatttcat-tatctaataaatgcag-----------------------
||||| ||||||||| ||||| || ||||||||||||| | | || || || ||||||||||| ||||||||||| || || || || ||  |  |||||||   |   ||||   ||  | |   |  ||   |    |  | |   ||||||   |||| ||| | ||  |  |    |  |  |  |   ||||                        
GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatctttcttctttcctttgtttatttttcttattttattaat---attcaagtctcatgaaaggcatcatagtaagttgcactttttgcttgcactgctatcttgacatggtttgcag

upper sequence: GRMZM2G458538_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 5'ss of exon 9

GTCTAGCATGCCAAATGGACAACCAAAGTGGCTTCTTTGTTTCATACCAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTTgtaagttgccaacttcaaacccatctcagtacttggaaagaaaacagttccattcaacagtcataaaaaggatactcatttcattatctaataaatgcag
 || | || ||| |||||||| || ||||||||||||| ||| || |||||||||||  |||| ||||||||||| || || || |||||| |  | |||||  |     |||         |||  | ||   |||  || | | | | | ||      |        | ||  | |  |  |||      |||||
ATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTAgtaagcagatt-tttccttgatgcttcaa-attttacaagtgaaaaatactaatgaatctctcttttttacttgcttgtgttgtcctctc-----tgcag

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|60338618|gb|DN205591.1|DN205591

EST:     CAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTT                         CTATCATACCGTGTGTTTGAGATCACAAACGTCTTGAAGTCGGCTTTTATC
genomic: CAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTTgtaagttgcc ... ataaatgcagCTATCATACCGTGTGTTTGAGATCACAAACGTCTTGAAGTCGGCTTTTATC

EST: gi|86465843|gb|DY232216.1|DY232216

EST:     CAGATTATCCTATGCTTAACTTCGTGCTTACTACAGCGATCTATCTTCTT                         CTATCATACCGTGTGTTTGAGATCACAAACGTCTTGAAGTCGGCTTTTATC
genomic: CAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTTgtaagttgcc ... ataaatgcagCTATCATACCGTGTGTTTGAGATCACAAACGTCTTGAAGTCGGCTTTTATC

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), 48 (downstream exon)
Score: 138

GTCTAGCATGCCAAATGGACAACCAAAGTGGCTTCTTTGTTTCATACCAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTTgtaagttgcc ... ataaatgcagCTATCATACCGTGTGTTTGAGATCACAAACGTCTTGAAGTCGGCTTTTATCCCCAGTAGGGATAATAGCCGCCTATACCAAAATTTGATTGCTGGGATCG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 216

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247