ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...gattgtgcattttgtgagcatgcactgaatatgatggatatgtttggaggaagcattattccaatttgatgataatggtgttatttacacttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGGGCACCAAGTTGTATTGTATTCTCAAGTCATGAGCAACTCCTGTGGGGCC

Basic information

species	Zea mays
transcript	GRMZM2G067299_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G067299_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g56580.1 (Oryza sativa), 3'ss of exon 2

gattgtgcattttgtgagcatgcactgaatatgatggatatgtttggaggaagcattattccaatttgatgataatggtgttat--ttacacttgttt--tcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGGGCACCAAGTTGTATTGTATTCTCAAGTCATGAGCAACTCCTGTGGGGCC
          ||    |  ||     |  | |||   |  | ||  |         |||   |  || |    ||   |||| |  | |   ||  ||   |||||||||||||| |||||  |||| |||||||||||| |||||   || | ||||||||  ||||| || ||||||||||||||| |||  ||||||||| 
----acttggttgactaaaatttttagtttgtgaccaaagtattatgtttccctcgtatgatatgtttacaggaaaaatgttttgatgatgttttcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCGGCACCAAACTGTATAGTCTTCTCAAGTCATGAGGAACATCTGTGGGGCA

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|149107346|gb|EE189225.2|EE189225

EST:     AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATG                         CTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG
genomic: AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG

EST: gi|78112747|gb|DV531141.1|DV531141

EST:     AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATG                         CTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG
genomic: AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG

EST: gi|211273588|gb|FL063642.1|FL063642

EST:     AAGCCGCCGCGAATCTCATCCTCAGCTACACCGGCACGTCGCCCTCCATG                         CTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG
genomic: AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG

EST: gi|149086246|gb|EE175786.2|EE175786

EST:     AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATG                         CTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG
genomic: AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG

EST: gi|149079157|gb|EE168093.2|EE168093

EST:     AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATG                         CTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG
genomic: AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG

EST: gi|71317285|gb|DR795328.1|DR795328

EST:     AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATG                         CTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG
genomic: AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG

EST: gi|94477323|gb|EB706281.1|EB706281

EST:     AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATG                         CTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG
genomic: AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG

EST: gi|71772065|gb|DR970002.1|DR970002

EST:     AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATG                         CTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG
genomic: AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG

EST: gi|94473867|gb|EB702825.1|EB702825

EST:     AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATG                         CTTGGCAAGGTACTGCGGCTCAGGAAGATTCTAAAAAACAAGTCGCAGCGG
genomic: AAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGG

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: 62

GGATGGGGTTCTGCAAGCCGCGGATGCCAAGGATTGGGTTTACAAGGGGGAAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctg ... ttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGGGCACCAAGTTGTATTGTATTCTCAAGTCATGAGCAACTCCTGTGGGGCC

Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 57

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 64

Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 37

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ggaggaagcattattccaatttgatgataatggtgttatttacacttgttttcagCTTGGCAAGGTACTGCGGCTCAAGAAGATTCTAAAAAACAAGTCGCAGCGGGCACCAAGTTGTATTGTATTCTCAAGTCATGAGCAACTCCTGTGGGGCC