ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttgtcatgtctgtgtgagcaactgagcatgcacaaggggattcacacaactaatttgactattggtgcatccgtgtag

Basic information

species	Zea mays
transcript	GRMZM2G071010_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G071010_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S60_129V6.1 (Physcomitrella patens), 5'ss of exon 4

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttgt-----catgtc------tgtgtgagcaactgagc-atgcacaaggggattcacacaactaatttga-ctattggtgcatccgtgtag----------------------------
  ||||||| ||||| |||||||||||||| || ||||| ||| |||| |||||||||||  ||||||| |||||    || ||    ||||||||| ||||||  ||| |     ||| ||      |   ||| |  ||   |  || |    | | ||| |  |  ||  |  | ||  ||    ||  | |||                             
ATTGAAGTTATTTTGCGACAAGGACTATCCCGACAAGCCTCCAACTGTTAGATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagatttatttgaccatttcacaactttcatgatcttcttttctgtgtatgttgcgtttctc-tagttacgtcaatctgctgtcatata-gagtaagcggccgcgaatgtaatatgttatccag

upper sequence: GRMZM2G071010_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ16450 (Selaginella moellendorffii), 5'ss of exon 3

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaa------tctttgtcatgtctgtgtgagcaactgagcatgcacaaggggattcacacaactaatttgac-----tattggtgcatccgtgtag---------
 || ||||||||||| |||||||| |||||||| ||||||||    || | ||||   || |||||||||||||| |||||    || || |  ||  | ||||        | | | |  | | | ||      ||     | | | ||  |||  |    |   |||||       | || |    ||||   |         
ACTTAAGTTGTTTTGCGACAAGGAGTATCCGGACAAGCCACCGAGCGTGAAATTCATGTCGAGAATCAACATGACCTGCGTCTCCCAAGACAATGGCGTTgtaagttgttcttcttttagttttctatgtctttttgtttcggaagatggctattaccttttcctctttgagggaagcactgatttgcccgtcatgatttctcag

upper sequence: GRMZM2G071010_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ17929 (Selaginella moellendorffii), 5'ss of exon 3

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaa------tctttgtcatgtctgtgtgagcaactgagcatgcacaaggggattcacacaactaatttgac-----tattggtgcatccgtgtag---------
 || ||||||||||| |||||||| |||||||| ||||||||    || | ||||   || |||||||||||||| |||||    || || |  ||  | ||||        | | | |  | | | ||      ||     | | | ||  |||  |    |   |||||       | || |    ||||   |         
ACTTAAGTTGTTTTGCGACAAGGAGTATCCGGACAAGCCACCGAGCGTGAAATTCATGTCGAGAATCAACATGACCTGCGTCTCCCAAGACAATGGCGTTgtaagttgttcttcttttagttttctatgtctttttgtttcggaagatggccattaccttctcctctttgagggaagcactgatttgcccgtcatgatttctcag

upper sequence: GRMZM2G071010_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ33318 (Selaginella moellendorffii), 5'ss of exon 3

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttgtcatgtc-tgtgtgagcaactgagcatgcacaaggggattcacacaactaatttgactattggtgcatccgtgtag--------------
 || |||||||  || ||||| ||||||||||| |||||||||  |||  ||||||| ||  ||||||||||||| |||||||||| |||||| |||   |||| |  |  ||| |  | | |  ||      |  |       ||  ||  ||| | | || | |||  ||  | |  |                    
ACTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGACTTGCGTTAATCGCGAGACTGGAGCTgtaagcactcgcattttgtttcttggctttgtggtctagtttctggtgtttccactagtgatcttacttgtgcagtaagcactcgctttttttttttgca

upper sequence: GRMZM2G071010_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ15952 (Selaginella moellendorffii), 5'ss of exon 3

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttgtcatgtc-tgtgtgagcaactgagcatgcacaaggggattcacacaactaatttgactattggtgcatccgtgtag--------------
||| |||||||  || ||||| ||||||||||| |||||||||  |||  ||||||| ||  ||||||||||||| |||||||||| |||||| |||   |||| |  |  ||| |  | | |  ||      |  |       ||  ||  ||| | | || | |||  ||  | |  |     |              
GCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGACTTGCGTTAATCGCGAGACTGGAGCTgtaagcactcgcattttgtttcttggctttgtggtctagtttctggtgtttccactagtgatcttacttgtgcagtaagcactcggcctccggtgttttc

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|33092413|gb|CF052407.1|CF052407

EST:     GATTCCACTCAAGAATCAACATGACATGCGTTAATCCCGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG

EST: gi|32805334|gb|CD957570.1|CD957570

EST:     TAATTACGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: TAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG

EST: gi|32908045|gb|CF012858.1|CF012858

EST:     GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG

EST: gi|5650118|gb|AI920478.1|AI920478

EST:     GATTCCACTCAAGAATCAACATGACATGCGTTAATCNCGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGGCTACNCG
genomic: GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG

EST: gi|5895802|gb|AW037048.1|AW037048

EST:     AACATGACATGCGTTAATCACGAGACAGGAGTG                         GGTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: AACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG

EST: gi|93013912|gb|EB639432.1|EB639432

EST:     GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG

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), 49 (downstream exon)
Score: 753

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACGATGGAGAACATCCTCACCCAGCTCAAGAAAGAGATGGCTGCCTCGCAGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1005

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1113