ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGTCCCGCTCTGGGAGCTCGTCTGGTTCTCGCTCGTCGCCAACACCTCCATCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAGgtacgcctttgctccgagtctgacagtaccaggcctacgccgggccatctatttggacctgggttgcttctgtgtggctcaagttgagaatctgcag

Basic information

species	Zea mays
transcript	AC194970.5_FGT005
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC194970.5_FGT005 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g39280.1 (Oryza sativa), 5'ss of exon 2

CGTCCCGCTCTGGGAGCTCGTCTGGTTCTCGCTCGTCGCCAACACCTCCATCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAGgtacgcctttgctccgagtctgacagtaccaggcctacgccgggccatctatttggacctgggttgcttctgtgtggctcaagttgagaa---tctgcag--------
|||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||| || |||||||||||||||||||| ||||| ||||||     |   | | ||  || |  |     ||||     |     | |||   | | ||   ||||  ||||||||| ||| || |||   ||||||         
CGTCCCGCTCTGGGAGCTCGTCTGGTTCTCCCTCGTCGCCAACACGTCCATCACCGGGATGAACCTTAGTCTCATGCTCAACTCCGTCGGTTTCTATCAGgtattgtatatttactaggttgcccattt---gcctggaatgt-ttgtatatgccgtcttg---tgctcttgtgtggctgaaggtgcgaaacctctgcaaacctgtag

upper sequence: AC194970.5_FGT005 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G45700.1 (Glycine max), 5'ss of exon 2

CGTCCCGCTCTGGGAGCTCGTCTGGTTCTCGCTCGTCGCCAACACCTCCATCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAGgtacgcctttgctccgagtctgacagtaccaggccta-cgcc-gggccatcta-tttggacctgggttgcttctgtgtggctcaagttgagaatctgcag--
 || ||  | ||||||||  | |||||||| || || ||||| |  || ||||| ||||||||| | |||||||||||||||||||| ||||||||||| ||| |  ||| ||   | | | ||| || || |   | |||  || |  | ||  ||  |  |   || ||| | |     |  |    | | |||      
TGTTCCTATGTGGGAGCTTATTTGGTTCTCACTGGTTGCCAATATGTCTATCACGGGGATGAACTTTAGCCTCATGCTCAACTCCGTTGGATTCTACCAAgtatggttttactttta-tatcaca-tatcatgttcatcgcttggactgtttaactttaattttcttttcttgtttagaatttcatccaatagtctttttaa

upper sequence: AC194970.5_FGT005 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G00210.2 (Glycine max), 5'ss of exon 2

CGTCCCGCTCTGGGAGCTCGTCTGGTTCTCGCTCGTCGCCAACACCTCCATCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAGgtacgcctttgctccgagtctgacagtaccaggcctacgccg-ggccatctatttggacctgggttgcttctgtgtggctcaagttgagaatctgcag-----
 || ||  | ||||||||  | |||||||| || || ||||| |  || ||||| ||||||||| | |||||||||||||||||||| ||||||||||| ||| |  |||    |  ||    |  |   | |  ||  |        ||| | |      |  || | ||       ||    || | ||||  |       
TGTTCCTATGTGGGAGCTTATTTGGTTCTCACTGGTTGCCAATATGTCTATCACGGGGATGAACTTTAGCCTCATGCTCAACTCCGTTGGATTCTACCAAgtatggttttatatcatgttcatcgcttggacggttaaactttaattttctttcttattaagaatttcatccaataatctt---tttaaaatccccttgcttc

upper sequence: AC194970.5_FGT005 (Zea mays), 5'ss of exon 2
lower sequence: PP1S116_49V6.1 (Physcomitrella patens), 5'ss of exon 3

CGTCCCGCTCTGGGAGCTCGTCTGGTTCTCGCTCGTCGCCAACACCTCCATCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAGgtacgcctt----tgctccgagtctgacagtaccaggcct-----acgccgggccatctatttg---gacctgg-gttgcttctgtgtggctcaagttgagaatctgcag---------------------------
  | ||  | |||||  |  |    |||||  | ||| | || || ||||||    | |||||||||||||||||||||||||| || || ||||| |||||  |   |     ||   ||  ||| ||||  |    ||     | || | | | | |  |||    | | |  | ||||    || |    |  | ||      | |                            
GATTCCTATTTGGGATTTATTTCTTTTCTCATTAGTCTCAAATACTTCCATCGTTAGTATGAACCTCAGCCTCATGCTCAACTCTGTGGGCTTCTATCAGgtcagtactgtcacgccatgaaactg-cagtcgcgattcttaatcatgctgtgacctttgattgcgaaatcagaagatgctctcttgcgatgtacttagatttcaagtaataacgttgtttctcgattgtgagacag

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|20803026|gb|BQ294076.1|BQ294076

EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTC
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAGgtacgccttt ... gaatctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTC

EST: gi|149098344|gb|EE184317.2|EE184317

EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTC
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAGgtacgccttt ... gaatctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTC

EST: gi|78087132|gb|DV515525.1|DV515525

EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTC
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAGgtacgccttt ... gaatctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTC

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), 46 (downstream exon)
Score: 76

CGTCCCGCTCTGGGAGCTCGTCTGGTTCTCGCTCGTCGCCAACACCTCCATCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGATTCTACCAGgtacgccttt ... gaatctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTCAACAGCAAGCACTACACCACTAAGGTCATATCCGCAGTCATCGTCGTGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121