ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatttatttagtcttatcttttgtgctttcttattttctatttaggagtgtatgatgtgtgacagtgccctttctctgttttaaaacaatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGACCTTGTTCTCGCCAATGGTGCATTGATGCCTCTGCTAGCCCAGTTGAATG

Basic information

species	Zea mays
transcript	GRMZM2G091119_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 4

------------gtatttatttagtcttat--cttttgtgctttcttattttctatttag--gagtgtatgatgtgtgacagtgccctttctctgttttaaaacaatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGACCTTGTTCTCGCCAATGGTGCATTGATGCCTCTGCTAGCCCAGTTGAATG
             |  | | ||    || |   || ||| ||| |||  | |   |||    ||||| ||  |  | |  | |    ||| |   | || ||| || |   |||||||| ||||| ||||||||||||||||| ||||| || ||||| |||||||||||||| ||||||||||||||| ||||||||||||| ||||||||||
gtatccgatcatctcctgacttgtctttgtgctttctgtacttccttgatattattttgattgagtgcattgttggagttattaatgtttttacctcttgaaaaaaaattgaagGCTGTATGGGCATTGGGCAATGTTGCTGGTGATTCCCCTAAGTGCCGTGACCTTGTTCTTGCCAATGGTGCATTGCTGCCTCTGCTAGCACAGTTGAATG

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G04430.1 (Glycine max), 3'ss of exon 4

gtatttatttagtcttatcttttgtgct-ttcttattttctatttaggagtgtatgatgtgtgacagtgccctttctctgttttaaaacaatacaaa---agGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGACCTTGTTCTCGCCAATGGTGCATTGATGCCTCTGCTAGCCCAGTTGAATG
   | | || |  | |   | | ||  |  |   |||   | ||| | | | |        || | | ||  |  |    |  ||||||  |  ||    |||| |||||||| ||||| ||||||||||| || ||||| ||||||||||| |||||||||  | |||||||  |||| || ||| | |||||||||||||
--gtatgttgatgcatgaatgtggtagtgctgacattacttgttttgaaattt--------tggccgagct-taccagaatactaaaactctgaaattccagGCAGTGTGGGCATTGGGGAATGTTGCTGGTGACTCTCCTAAGTGTCGTGATCTTGTTCTCAGCCATGGTGCCCTGATCCCACTGTTGGCCCAGTTGAATG

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G16143.1 (Arabidopsis thaliana), 3'ss of exon 3

-----gtatttatttagtcttatcttttgtgctttcttat--tttctatttaggagtgtatgatgtgtgacagtgccct-----ttctctgttttaaaaca-----atacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGACCTTGTTCTCGCCAATGGTGCATTGATGCCTCTGCTAGCCCAGTTGAATG
      ||| | ||||   || | | |  ||  |   |||  | || |||| |     | |   |    |   ||  ||     || | |||||   ||       ||    |||||||||||||| || || ||||||||||| ||||||||   |||  | || ||||| || |   | || || ||||| ||  | ||  | ||||||||||
gtaagatatgtgtttatggttttttctcatgactcaatatactgtcaattttgtttgttttcgggaacaagcatgttctaaagcttgtttgtttcttaatcttttcatgtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGATCTTGTCCTTGGTCAAGGAGCTTTGATACCATTACTCTCTCAGTTGAATG

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 4

gtatt-tatt-tagtcttatcttttgtgctttcttattttctatttaggagtgtatgatgtgtgacagtgccc-tttctctgttttaaaacaatacaaa-agGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGACCTTGTTCTCGCCAATGGTGCATTGATGCCTCTGCTAGCCCAGTTGAATG
|| |   ||| |  ||||    |  |||   |  | || || | |  ||| |  ||| ||       |||||   ||  |||||   |  |  |   || ||||||| ||||||||||| || |||||||| ||||| ||||| || |||||||||||| | |   |||| || |||||||||||||| || ||| | |  |
gtttcacattgtgatctttagctaggtgtcatgcttttgtcgact--ggatttcatgctgaccagttgtgccgacttgactgttaatattctctttgaacagGCTGTATGGGCTTTGGGAAACGTTGCTGGTGATTCGCCGAAATGCCGTGACCTTGTTTTAGGTCATGGGGCCTTGATGCCTCTGCTTGCGCAGCTTACGG

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ38593 (Selaginella moellendorffii), 3'ss of exon 4

gtatttatttagtcttatcttttgtgctttcttattttctatttaggagtgtatgatgtgtgacagtgccctttctctgttttaaaacaatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGACCTTGTTCTCGCCAATGGTGCATTGATGCCTCTGCTAGCCCAGTTGAATG
                       ||| ||| || | || |||||   |  |  ||   | |||||       ||  |||           |||   |||| || |||||| | ||||||||||||||||| ||||||||||| || || || ||  |    |    |||  |||||||  ||||||| ||| |||| |
-----------------------gtgattttttctcttgtatttccaaa-gcttggaatctgaca-------tttcctg----------gtaccgcagGCAGTATGGGCTCTTGGCAATGTTGCTGGCGACTCTCCGAAGTGCCGAGATCTCGTCTTGAATAGCAATGCCATGATGCCGTTGCTAGCACAGCTGAACG

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|211097395|gb|FL161930.1|FL161930

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|148930623|gb|EE285320.2|EE285320

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|149036989|gb|EE155227.2|EE155227

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|26457325|gb|CA828908.1|CA828908

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|211097396|gb|FL161931.1|FL161931

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGTTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTTGGGCA-TGTTGCTGGCGATTTCTCCGAAGTGTCGTG
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTT-GGGCAATGTTGCTGGCGATT-CTCCGAAGTGTCGTG

EST: gi|211099874|gb|FL161945.1|FL161945

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|211092445|gb|FL161903.1|FL161903

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAAATGT-GCTGGCGATTCTCCGAAGTGTCGTGA
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAA-TGTTGCTGGCGATTCTCCGAAGTGTCGTGA

EST: gi|22521415|gb|BU080226.1|BU080226

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|211089987|gb|FL161898.1|FL161898

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCA-TGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|211092447|gb|FL161905.1|FL161905

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|89252976|gb|DY624762.1|DY624762

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|149015249|gb|EE045043.2|EE045043

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|149067410|gb|EE286973.2|EE286973

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|211092451|gb|FL161909.1|FL161909

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|211097406|gb|FL161941.1|FL161941

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCCGA-GTGTCGTGA
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCC-GAAGTGTCGTGA

EST: gi|211094922|gb|FL161920.1|FL161920

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|148982771|gb|EE028594.2|EE028594

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

EST: gi|148931614|gb|EC874737.2|EC874737

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGAC

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: 805

TTCTGGCACTTCAGAAAATACAAAGGTTGTTATTGATCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattt ... aatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGACCTTGTTCTCGCCAATGGTGCATTGATGCCTCTGCTAGCCCAGTTGAATG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 298

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 378

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taggagtgtatgatgtgtgacagtgccctttctctgttttaaaacaatacaaaagGCTGTGTGGGCTTTGGGCAATGTTGCTGGCGATTCTCCGAAGTGTCGTGACCTTGTTCTCGCCAATGGTGCATTGATGCCTCTGCTAGCCCAGTTGAATG