ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcag

Basic information

species	Zea mays
transcript	GRMZM2G127338_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G13710.1 (Glycine max), 5'ss of exon 1

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctg-----agcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcag-------------------------------------------------------------------------------------------------
  |||||||| |||||||||||||| || || ||||||||||| ||  | || || || || ||||| ||  |||| ||||||||||| ||||| || ||||     |     ||   |   ||  |       ||  | | | | ||     || |   ||   ||  || || | ||  |   ||   ||  | ||                                                                                                     
CCAGGAACGCAAAGTGGTGGTACTCTGCTTTTCACAATGTCACTGCTGTTGTTGGAGCTGGTGTGCTGGGTTTCCCATACGCCATGTCAGAGCTAGGATGgtaatctcatcttctcttttcatgcctcatcacttcctaataaatatgtatccagagtttttttcttgtatatacc-taaaaacacacttattaaaatatcaatgaatagaaaaaaaaattattattatggagtgtttatactgtatcattattctattgttatggccttcatgcatgcatgtttctttgttgtggcag

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA16G06750.1 (Glycine max), 5'ss of exon 1

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctag--cttgctagctgtgtgcctgtgtctgactgac-----tctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcag
  ||||| || || ||||||||||| ||||||||||||||||| |||||||| || || || || ||  | ||||| || |||||||| ||||| || ||||   | |   |   |    |  |  | ||||| | ||| | | |      | | | |    ||  || | ||  || ||  ||    | | |   || |    
CAAGGAATGCAAAATGGTGGTACTCTGCCTTCCACAATGTCACTGCCATGGTTGGTGCTGGTGTTCTTAGTCTCCCATATGCCATGTCTGAGCTTGGATGgtatatccctcaaacccaagttacattttgcctttttcttattaaagattgtttaaacatcttttgatcacata-attatg-cacaaaaggtaaaaatgttt--

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT5G40780.2 (Arabidopsis thaliana), 5'ss of exon 2

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcag
  || || || |||||||||||||| || || ||||||||||||||||||||||| ||||| || || || ||||| |||||||||||  ||||||| ||||   | | |         | | |  |   | |  || |       | | |     | ||   | | ||   | |  | |  | ||           
CAAGAAATGCAAAGTGGTGGTACTCTGCTTTTCACAATGTCACCGCCATGGTCGGTGCCGGAGTTCTTGGACTCCCTTACGCCATGTCTCAGCTCGGATGgtaaattcccctaaaccaaaaccggtttattttacctaaaccggatttatcaaatcttaaccggttttaatttgtttt-cttttcag----------

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0010g02640.t01 (Vitis vinifera), 5'ss of exon 5

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctgagcgc--gcttaaattagatgtatcatatcatgccatgcatgcatatgcag------
   ||||||| || ||||||||||| || ||||||||||| ||||||||||| || || ||||| ||| | ||||| |||||| || | | |||||| ||||  ||       | || |   |   | |||     |||    |  | |||     |||  | || |       |||  | |      ||  | |  |       
CCCGGAACGCGAAATGGTGGTACTCTGCATTCCACAATGTGACCGCCATGGTTGGGGCTGGCGTCCTCAGTCTCCCTTACGCCGTGGCAGGGCTCGGATGgtatgttt-----cctgtttctttcattcctaaaaatgaaattccttcagcttttactttgaatataaaagctttattgtcctgaaattgggttttgattctgtt

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv14s0171g00400.t01 (Vitis vinifera), 5'ss of exon 2

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctag---cttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcag
  ||||| || || |||||||| || || ||||||||||| || ||||||||||| || || || ||||| ||||| ||||||||||||||||| || ||||  ||    |      || | ||   |       |   |   |   |||||   |  || | | || |  | ||||  |    ||       | | |||
CCAGGAATGCAAAATGGTGGTATTCAGCATTCCACAATGTTACTGCCATGGTCGGAGCTGGTGTCCTCGGTCTCCCTTACGCCATGTCCGAGCTTGGATGgtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataa-aaaaaatattgatcttttcag

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0010g02660.t01 (Vitis vinifera), 5'ss of exon 1

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctagcttgctagctgtgtgcctgtgtctg--actgactctgagcgcgcttaaattagatgtatcatatcatgcc-atgcatgcatatgcag-----
   ||||||| || ||||||||||| || ||||||||||| ||||||||||| || || ||| | ||| | ||||| ||||||||| | | ||| || ||||  ||       | || |   |   | |||     ||  |||   || |      ||| || || |  |    |||  |    |  |  |  | ||        
CCCGGAACGCGAAATGGTGGTACTCTGCATTCCACAATGTGACCGCCATGGTTGGGGCTGGCATCCTCAGTCTCCCTTACGCCATGGCAGGGCTTGGATGgtatgttt-----catgtttctttcattcctaaaaatggaactccttcagcatttacttcaaatataaatgctttattgtcttgaaactcggctttgatattgtt

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0010g02700.t01 (Vitis vinifera), 5'ss of exon 1

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtat-catatcat-gccatgcatgcatatgcag--------
  |||||||| || ||||||||||| || ||||| ||||| ||||||||||| || || ||||| ||| | ||||| ||||||||| | | ||| || ||||  ||       | || |   |   | |||     |||   ||||  |   || |||  ||  ||  |  |   | || | | || |      |   |        
CCAGGAACGCGAAATGGTGGTACTCTGCATTCCATAATGTGACCGCCATGGTTGGGGCTGGCGTCCTCAGTCTCCCTTACGCCATGGCAGGGCTTGGATGgtatgttt-----catgtttctttcattcctaaaaatga--aactcctacaacgtttactttgaatacaaacgctttattgtcctgaaactgggttttgattctgtt

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: PP1S5_176V6.1 (Physcomitrella patens), 5'ss of exon 2

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgct----agcttgctagctgtgtgcctgtgtctgactgactctgagcgc-gcttaaattagatgtatcatatcatgccatg--catgcatatgcag
   | || ||||| |||||||||||||||||||||||||| ||||| ||||| |||||||| ||||| ||  | ||| ||||||||  | |  |    ||||| |  | |        |||     |  ||  | | |||  || |  ||     || | ||     ||  |   ||  | | |  |||   || || ||||||
ATCGCAAAGCCAAATGGTGGTACTCCGCCTTCCACAATGTTACCGCAATGGTGGGCGCCGGAGTGCTGGGATTGCCCAACGCCATGGTCTACTTAACATGgtgagggctcctcacgttttgtctaatccgtctcagagtcacacagtttcatgttgcagtttgcggcagtgggcacaagtaacggaatggctattcacatgcag

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ10949 (Selaginella moellendorffii), 5'ss of exon 1

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcag
 |||||||||||| |||||||||||||| || ||||| || ||||| ||||| ||  | |||||||| |   | ||||  || |||    | || || ||||    ||| | |  || ||     ||     | | | |  |  |||  |       |                                       
CGAGGAACGCCAAATGGTGGTACTCCGCGTTTCACAACGTAACCGCGATGGTAGGATCGGGCGTGCTGGCGTTACCCTCGGCTATGGTTTATCTGGGATGgta---acgttcgaatgtta-taacgtctacattttttag-ggttcttcgtttttccag--------------------------------------

upper sequence: GRMZM2G127338_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ10950 (Selaginella moellendorffii), 5'ss of exon 2

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcag--------
  ||||||||||||||||||||||| |||||||| ||||||||||||||||| || || || || ||  |||||||||  || |||  | | || |||||||  || |      | ||      | | | | |   |  ||  ||   |   ||||||  || |||  |   | |    |  |   ||  |   ||         
CCAGGAACGCCAAGTGGTGGTACTCGGCCTTCCATAATGTCACCGCCATGGTTGGAGCTGGAGTTCTTAGCCTCCCCTCGGCGATGGTCTATCTTGGCTGgtaagttc-----ttcgcagctcttcttcgtttcaatcgctagcttcaaattcgcttagtttcgatccaaattcttggtcagtcagtgttttctcattcgtgctc

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|211348400|gb|FL389761.1|FL389761

EST:     GTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTG                         GGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgc ... gcatatgcagGGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACAC

EST: gi|211044250|gb|FL124840.1|FL124840

EST:     GTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTG                         GGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgc ... gcatatgcagGGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACAC

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 3 RNA-Seq libraries.

Block sizes: 42 (upstream exon), 22 (downstream exon)
Score: 3

GGAGGAACGCCAAGTGGTGGTACTCCGCCTTCCACAATGTCACCGCCATGGTCGGCGCCGGCGTGCTCGGCCTCCCCTACGCCATGTCCGAGCTCGGCTGgtgcgtacgc ... gcatatgcagGGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTCCCGGGCAAGCGCTTC

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