ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcccctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G112609_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G112609_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 1

GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcccctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcag
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||               |||||||||||||||||||||||   |   | |||| |   |   |||       ||  ||   ||   || ||    |  |||   | || | |     |||||  || ||| || | | |||                        
GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgt---------------ctctctctctctctctctctctccgcccgcccctctttacatgattctactctctcctcgatctggtgcttgtttgagt--gcctgcgctgatgg----cctaat--gccctccttgcct-cgcag----------------------

upper sequence: GRMZM2G112609_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G27600.1 (Glycine max), 5'ss of exon 1

GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcccctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcag
 ||||| || ||||| || || |||||   |||||||||| |||||||||||||||| |||||||| ||||| ||||||||  |||| ||| |||| || |||    | ||   | | || ||||| || |     | ||  |   | | |     | | | | | |   | |  ||  |   || ||     | |||                                                                   
AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCCGTCATCACGCGCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGATgtaaacccccttttttcatc-ctctcacttttagggtttccattattattttctaatttatttttatgaattcggtgcgtct-aatttggatacattcattt---------------------------------------------------------------

upper sequence: GRMZM2G112609_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA15G11350.3 (Glycine max), 5'ss of exon 1

GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcccctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcag
 ||||| || ||||| || || |||||   |||||||||  ||||||||||||| || |||||||| ||||| ||||||||| |||| ||  |||| || |||     || || | | || | ||||| || |     | ||    | | | | | | |   |      |  |  ||| | ||   |  |  | |||     ||                                                             
AATGGCTCAAGCGGTTGAAGAATGGTATAAGCAGATGCCTGTCATCACGCGCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGATgta----atcccctttcttcgcactctcacttttagggtttccaattttatttttttatgaattcggtgcgtc--tgatttgggtttattcttttttaatatctcg-----------------------------------------------------------

upper sequence: GRMZM2G112609_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv00s0704g00010.t01 (Vitis vinifera), 5'ss of exon 1

GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcccctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcag
 ||||| || || || || || ||||||  ||||||||| |||||||| ||||| || |||||||||||  ||||||||||| |||| ||| | ||||| |||      |||  |  || ||   || | ||  | | ||  | |   |   |||   |   || ||       | |  |   |   | ||   |||||                                                                  
AATGGCTCAAGCCGTTGAAGAATGGTACAAGCAGATGCCAATCATCACCCGCTCTTATCTCACCGCCGCAATCGTCACCACCATCGGTTGCTCTCTCGACgtat---gcctctgtatctttcaggctttttcgatgtatcggtgtgcattattcttgtttattcccttgtgtggagggttgatagggtttttgttttcgatgt--------------------------------------------------------------

upper sequence: GRMZM2G112609_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ29912 (Selaginella moellendorffii), 5'ss of exon 1

GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcccctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcag
 ||||||||   ||| |||||||||||| |||| || || |||||||||||||||||||||||     ||||  |||| || |  || ||| | || || |||    |||| |     | |       |     | | |       | | | ||||| | |   | | |||     |  |||                                                                                   
AATGGCGCAATTGGTAGAGGAGTGGTACAGGCAAATACCTATCATCACGCGCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctcttctcttgtttggagtgtttggagtgttttctctaatttttttctctttgttcttttttctggtgcgtgtag-----------------------------------------------------------------------------------

upper sequence: GRMZM2G112609_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ25138 (Selaginella moellendorffii), 5'ss of exon 1

GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcccctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcag
 ||||||||   ||| |||||||||||| |||| || || |||||||||||||||||||||||     ||||  |||| || |  || ||| | || || |||    |||| |     | |       |     | | |       | | | | ||||| | |   | | ||   ||  |                                                                                     
AATGGCGCAATTGGTAGAGGAGTGGTACAGGCAAATACCTATCATCACGCGCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctcttctcttgtttggagtgtttggagtgttttctctaatttttttttctctttgttcttttttctggtgcgtgtag---------------------------------------------------------------------------------

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|76917920|gb|DV167073.1|DV167073

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|37422155|gb|CF648783.1|CF648783

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|37421964|gb|CF648686.1|CF648686

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|91048268|gb|EB158686.1|EB158686

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|211475584|gb|FL117463.1|FL117463

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|32919420|gb|CF024232.1|CF024232

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|211475588|gb|FL117467.1|FL117467

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|50333879|gb|CO529005.1|CO529005

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|6637090|gb|AW261362.1|AW261362

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|211475590|gb|FL117469.1|FL117469

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|56382233|gb|CV984902.1|CV984902

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGNGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|76012317|gb|DT939487.1|DT939487

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|211473078|gb|FL117461.1|FL117461

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCAC-GTCGGCTCCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|91878613|gb|EB408570.1|EB408570

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|148970116|gb|EE021054.2|EE021054

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|211475589|gb|FL117468.1|FL117468

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|60342635|gb|DN209608.1|DN209608

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCAAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

EST: gi|211475586|gb|FL117465.1|FL117465

EST:     GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAA                         ATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCAC

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: 209

GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctc ... ggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCACTACGAGATTTGGCGCCTCGTCACTAACTTCCTCTACTTCCGCAAGATGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168