ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAAGCTATGGAGAAGGCTGTGAAGAACAAAGTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatgttcctagctagttcttttactccctgatttcgcaagttcttgtaaactcttaccaacatgtttcctctgctag

Basic information

species	Zea mays
transcript	GRMZM2G068755_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G068755_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 4

GAAGCTATGGAGAAGGCTGTGAAGAACAAAGTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatgttcctagctagttcttttactccctgatttcgcaagttcttgtaaactcttaccaacatgtttcctctgctag
||| | |||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||| ||||| ||||| | || ||| |   | |||  |  |||| | |      || |||||     | |  ||||| |||| ||| ||||
GAATCAATGGAGAAGGCTGTAAAGAACAAAGTGGCCAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAGGCACTTAGgtaagctcatagttgtatttttgccatcctgttatattttttttttgta---cttcattaacatctttcttctactag

upper sequence: GRMZM2G068755_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g60050.1 (Oryza sativa), 5'ss of exon 4

GAAGCTATGGAGAAGGCTGTGAAGAACAAAGTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatgttcctagctagttcttttactccctgatttcgcaagttcttgtaaactcttaccaacatg-tttcctctgctag
||| | |||||||||||||| ||||||||| |||||||||||||||| |||||||| ||||| |||||||||||||| ||||| |||||||  |  |   | || | |     | |     ||  | |  ||  | |  |||||  ||||  || ||||
GAATCAATGGAGAAGGCTGTAAAGAACAAAATGGCTAAAGCAGTTGTGCCTGCTATCGATGTAATGTTTCAAGCACTTAGgtaagttcctacttcctaactgtatttctgccatcctgttatttgtctgtaccttcattaacataatttctcctactag

upper sequence: GRMZM2G068755_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 4

GAAGCTATGGAGAAGGCTGTGAAGAACAAAGTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatg----ttcctagct-----agttcttttactccctgatttcgcaagttcttgtaaactct-taccaacat-gtttcctctgctag---
|| || |||||||| ||  | || |||||||| |||||||| || |||||||| || ||||| |||||||||||  |||||| ||     || | | |     |  | |  ||||      |||      || || | ||   | ||| |  ||  |||  | ||||     
GATGCAATGGAGAAAGCGATAAAAAACAAAGTTGCTAAAGCGGTGGTACCTGCAATAGATGTTATGTTTCAAGCTTTAAGgtttggaatctctttgatgcaacatatataatacttgtctcttttttttttttttatgaatcttatacaattattattttttatgctgctag

upper sequence: GRMZM2G068755_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 4

GAAGCTATGGAGAAGGCTGTGAAGAACAAAGTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatg----ttcctagct--agttcttttactccctgatttcgcaagttcttgtaaactcttaccaacat-gtttcctctgctag---
|| || |||||||| ||  | || |||||||| |||||||| || |||||||| || ||||| |||||||||||  |||||| ||     || | | |  |     | || | | ||  ||      || ||  || ||  ||| |  ||  |||  | ||||     
GATGCAATGGAGAAAGCAATAAAAAACAAAGTTGCTAAAGCGGTGGTACCTGCAATAGATGTTATGTTTCAAGCTTTAAGgtttggaatctctttgttgcaacatatataatacttgtctttttcttttttttgaatcttatacaattattattttttgtgctgctag

upper sequence: GRMZM2G068755_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv10s0116g00490.t01 (Vitis vinifera), 5'ss of exon 4

GAAGCTATGGAGAAGGCTGTGAAGAACAAAGTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatgttcctagctagttctttt--actccctgatttcgcaagttcttgtaaactcttaccaacatgtttcctctgctag-------
|| || |||||||| ||  | || |||||||| || ||||||||||||||||| |||||||| ||||| ||||| ||||||| ||| | | | |   | |  |  |  | ||| |||      | |||      | || |  || |  ||  | || | |       
GATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCTGCCATTGATGTTATGTTCCAAGCCCTAAGgtttgtgcattgatttctttgctggaaactctgctttattttatgcttagctgatttt-cagacttcattgttgtgtttgtaatcag

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|211517040|gb|FL438272.1|FL438272

EST:     TTCAAGCACTAAG                         CGAATTTGGAACTAAGGTAGTGCCACCCAAAAAGATTCTGAAGATGCTACC
genomic: TTCAAGCACTAAGgtatgttcct ... cctctgctagCGAATTTGGAACTAAGGTAGTGCCACCCAAAAAGATTCTGAAGATGCTACC

EST: gi|71441120|gb|DR822170.1|DR822170

EST:     GTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAG                         CGAATTTGGAACTAAGGTAGTGCCACCCAAAAAGATTCTGAAGATGCTACC
genomic: GTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatgttcct ... cctctgctagCGAATTTGGAACTAAGGTAGTGCCACCCAAAAAGATTCTGAAGATGCTACC

EST: gi|32934909|gb|CF039721.1|CF039721

EST:     ACCTGCTATTGATGTGATGTTTCAAGCACTAAG                         CGAATTTGGAACTAAGGTAGTGCCACCCAAAAAGATTCTGAAGATGCTACC
genomic: ACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatgttcct ... cctctgctagCGAATTTGGAACTAAGGTAGTGCCACCCAAAAAGATTCTGAAGATGCTACC

EST: gi|211192783|gb|FL428804.1|FL428804

EST:     ATGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAG                         CGAATTTGGAACTAAGGTAGTGCCACCCA
genomic: GTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatgttcct ... cctctgctagCGAATTTGGAACTAAGGTAGTGCCACCCA

EST: gi|30591281|gb|CD052294.1|CD052294

EST:     GTGGCTAAAGCAGTTGTACCTGCTATTGATG--ATGTTTCAAGCACTAAG                         CGAATTTGGAACTAAGGTAGTGCCACCC
genomic: GTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatgttcct ... cctctgctagCGAATTTGGAACTAAGGTAGTGCCACCC

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: 87

GAAGCTATGGAGAAGGCTGTGAAGAACAAAGTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAGgtatgttcct ... cctctgctagCGAATTTGGAACTAAGGTAGTGCCACCCAAAAAGATTCTGAAGATGCTACCTGAGCTGTTTGACCATCCAGACCAGAATGTCCGGGCTTCTTCTAAGGGT

Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 33

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26