ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaggagcacagccgcaacctttgcccccacttttttttttatctctatttctgtttcttctctccaaatgtttttcgtttttgttcaatgctaatggtgtgccatttgtctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGAAGTGGCCCCCTGGTTAAATTACGAAGGGTGACATGTTTGATTTCCTGTA

Basic information

species	Zea mays
transcript	GRMZM2G143767_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G143767_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g45660.1 (Oryza sativa), 3'ss of exon 5

----------------------------------------------------------------gtaaggagcacagccgcaacctttgcccccacttt---tttttttatctctatttctgtttc--ttctctccaaatgtttttcgtttttgt-tcaatgctaatggtgtgccatttgtctgtc-acagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGAAGTGGCCCCCTGGTTAAATTACGAAGGGTGACATGTTTGATTTCCTGTA--
                                                                |||   |    |  |   | | ||   |  | |||   | ||  || |  |  |  ||  |    ||| | | |  |   |   |||  || |  ||||||||  |||  |||   |||||| ||||| ||||| |||||||| |||||| |||||||||| ||||||||||||||||| |||||  |||| ||| | || |||  ||  ||| ||  | | || |   
gtaagcactcccatgccacatctcttttctacttactggggtttgcacatgttttcacttttcagtatacatgctacacatcatccttcaacgtattttcggtgttgatacccatgctcatgcatgagctcttttccaccgccatatttttcagtatttatgctaatactgtatcatcgctctgtccacagGTCAATCAGTCTATCACCTGCACTTGCATGTACTAGGTGGAAGGCAGATGAAATGGCCTGCTGGCTAATTAACCAAG--TGGGATGCTTTCTGTACTATTGC

upper sequence: GRMZM2G143767_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G17330.1 (Glycine max), 3'ss of exon 5

gtaaggagcacagccgcaa-cctttgcccccacttttttttttatctctatttctgtttcttctctccaaatgtttttcgtttttgttcaatgctaatggtgtgccatttgtctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGAAGTGGCCCCCTGGTTAAATTACGAAGGGTGACATGTTTGATTTCCTGTA-
               | || ||  ||   |   ||     |||||||  || | | |  |||   |  |   ||  | |   |     |||   | ||  | | |  ||| | |     ||| |||||||| |||||||||||| |||||||| | ||||| || |||||||| ||||| ||||||| ||      |   | || | ||  ||||    |  
---------------gtaagcccctgtttcttgttaacaatttatctggatctttttcacttgcttata---gtgctgccactacccacaaactttatcttatactctttattttgattagGTCAATCTGTGTATCATCTGCACTTGCATGTATTAGGTGGCAGACAGATGAATTGGCCACCTGGTTGAAG-GTTGACTATTACTTTTTAAATTTTAACTGC

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|6536550|gb|AW224863.1|AW224863

EST:     AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGAT                         GCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTG
genomic: AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGATgtaaggagca ... tctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTG

EST: gi|60340294|gb|DN207267.1|DN207267

EST:     AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGAT                         GCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGA
genomic: AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGATgtaaggagca ... tctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGA

EST: gi|161590785|gb|EY958727.1|EY958727

EST:     GTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGGAAGGAT
genomic: GTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTG-AAGGAT

EST: gi|211478451|gb|FL136940.1|FL136940

EST:     AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGAT                         GCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTG
genomic: AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGATgtaaggagca ... tctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTG

EST: gi|211478447|gb|FL136936.1|FL136936

EST:     AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGAT                         GCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGA
genomic: AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGATgtaaggagca ... tctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGA

EST: gi|211478453|gb|FL136942.1|FL136942

EST:     AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGAT                         GCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGA
genomic: AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGATgtaaggagca ... tctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGA

EST: gi|211376140|gb|FL136932.1|FL136932

EST:     AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGAT                         GCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGA
genomic: AGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGATgtaaggagca ... tctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGA

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), 45 (downstream exon)
Score: 20

GAAATCCTGGGCCGGCTCCTTTACGCAGCGAAAGTAGTGGCAGAAAAGGAAGGTGTAGCGAGTGGGTACCGTGTTGTCATCAACAATGGTGCTGAAGGATgtaaggagca ... tctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGAAGTGGCCCCCTGGTTAAATTACGAAGGGTGACATGTTTGATTTCCTGTA

Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 19

Block sizes: 48 (upstream exon), 19 (downstream exon)
Score: 5

Block sizes: 43 (upstream exon), 26 (downstream exon)
Score: 10

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ccaaatgtttttcgtttttgttcaatgctaatggtgtgccatttgtctgtcacagGCCAATCTGTCTATCATCTGCACCTGCATGTACTTGGTGGAAGGCAGATGAAGTGGCCCCCTGGTTAAATTACGAAGGGTGACATGTTTGATTTCCTGTA