ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgcagtttttactcaaattggtatttgtttttagatttttattatcatcatgcataccagactgagcacacttttttctctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAGGACTTCATGCCAACATTCCCTGCTCTTAATGAAC

Basic information

species	Zea mays
transcript	GRMZM2G179097_T07
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G179097_T08 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 6

-----gtgcagtttttactcaaattggtatttgtttttagatttttattatcatcatgcataccagactgagcacacttttttctctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAGGACTTCATGCCAACATTCCCTGCTCTTAATGAAC
     ||||   |  || |    ||   ||   ||| ||   |    | ||  | |   |   ||  |||||||||| | |||      |||||||  |||||||||| | |||| |  ||||  | ||||||  |||||||||||| |||||||||||||| ||||||||||||||||||||||| |||||| 
gtaatgtgctactgctattttttttttcatg-atttatatcatgcattcatatttaaatacttcaatctgagcacacctgttttggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAAT

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|44681705|gb|CK786753.1|CK786753

EST:     AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAG                         CGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT

EST: gi|32847543|gb|CD987224.1|CD987224

EST:     AAGCTGGTTTTGATCTATTGAACAGATTGCTGACTTATGACCCTGATAAG                         CGCATATCAGCAGACGATGCTCTGAAGCACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT

EST: gi|32932651|gb|CF037463.1|CF037463

EST:     AAGCTGGTTTTGATCTATTGAACAGATTGCTGACTTATGACCCTGATAAG                         CGCATATCAGCAGACGATGCTCTGAAGCACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT

EST: gi|32832598|gb|CD972276.1|CD972276

EST:     AAGCTGGTTTTGATCTATTGAACAGATTGCTGACTTATGACCCTGATAAG                         CGCATATCAGCAGACGATGCTCTGAAGCACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT

EST: gi|32930695|gb|CF035507.1|CF035507

EST:     AAGCTGGTTTTGATCTATTGAACAGATTGCTGACTTATGACCCTGATAAG                         CGCATATCAGCAGACGATGCTCTGAAGCACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT

EST: gi|60394713|gb|DN227583.1|DN227583

EST:     AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAG                         CGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT

EST: gi|60345354|gb|DN212327.1|DN212327

EST:     AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAG                         CGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT

EST: gi|60354973|gb|DN221946.1|DN221946

EST:     TTTTGATCTA-TGAAACAGACTGCTGACTTATGACCCTGATAAG                         CGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT
genomic: TTTTGATCTATTG-AACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCT

EST: gi|32932744|gb|CF037556.1|CF037556

EST:     AAGCTGGTTTTGATCTATTGAACAGATTGCTGACTTATGACCCTGATAAG                         CGCATATCAGCAGACGATGCTCTGAAGCACAAATGGTTCTCTGAA
genomic: AAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAA

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: 48 (upstream exon), 38 (downstream exon)
Score: 28

AAGGGATAAGTTCCCAGCCGCTTCTTTTTCTGGGCGACCAATCCTGTCTGAAGCTGGTTTTGATCTATTGAACAGACTGCTGACTTATGACCCTGATAAGgtgcagtttt ... tctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAGGACTTCATGCCAACATTCCCTGCTCTTAATGAAC

Block sizes: 29 (upstream exon), 38 (downstream exon)
Score: 19

Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 34

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 19

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gatttttattatcatcatgcataccagactgagcacacttttttctctcgtacagCGCATATCAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAGGACTTCATGCCAACATTCCCTGCTCTTAATGAAC