ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcatatctgtttctgatactgtttcagtcatgtatgcattccttgtagataggttgataccttagtgacattgatcacttgtaatggaatcgctcaattttgctgtggacatgaaatcttgtctgttaattgctgtgattccag

Basic information

species	Zea mays
transcript	GRMZM2G061745_T02
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G061745_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 9

TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcatatctgtttctgatactgtttcagtcatgtatgcattccttgtagataggttgataccttagtgacattgatcacttgtaatggaa--tcgctcaattttgctgtggacatgaaatcttgtctgttaattgctgtgattccag
| ||||||||||| ||||||||||| |||||| |||||||||| |||||||| ||||| || || || || || ||||| || |||||  |||  | ||||| |                    |||  |||   | ||||      |  |  |  | || | |  ||| || |  |   |  ||  |  ||||   |   |                                    
TTAAAACAAACGATATGATGTTGGTCATATACTTGTCTTCTCTTATCCGGAGTGTCATCGCACTCCATAACTTGATCAATAACAAGgtaaatt-gtttctgtct--------------------tatctattgaatatagaagatgcgggagttaggagatacttgtcatttattgtaagacttccttttatttgattccag------------------------------------

upper sequence: GRMZM2G061745_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 9

TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcatatctgtttctgatactgtttcagtcatgtatgcattccttgtagataggttgataccttagtgacattgatcacttgtaatgga-atcgctcaattttgctgtggacatgaaatcttgtctgttaattgctgtgattccag
|||||||||||||||||||||||||||| ||||||||||| || || ||||| || |||||  | |||||  | || || || |||||  |   | || | ||  |||  |||       ||| | |   ||  |  |      | ||||    ||  |  | |  || ||| ||  | | |||      | |  ||                                        
TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgtata---agattt-ttgttgaggctgcc-----catttctaagtttttaatgatgtagctgatgatata-cgctaat--tctcttttagcgtatatcatcagctatcactc---------------------------------------

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|32937292|gb|CF042111.1|CF042111

EST:     CTTCTCTGATCCGGAGCGTCATTGCGCTTCCCAATTTAATCAACAATAAG                         ATGCTAAACAAGGAGCCCGAGAAGGCCGAGGATTCGAAACCAACCGCCATT
genomic: CTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcat ... gtgattccagATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT

EST: gi|32943105|gb|CF047924.1|CF047924

EST:     CTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG                         ATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT
genomic: CTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcat ... gtgattccagATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT

EST: gi|32932870|gb|CF037682.1|CF037682

EST:     CTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG                         ATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT
genomic: CTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcat ... gtgattccagATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT

EST: gi|4730759|gb|AI649925.1|AI649925

EST:     TGATCCGGAGCGTCATTGCGCTTCCCAATTTAATCAACAATAAG                         ATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT
genomic: TGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcat ... gtgattccagATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT

EST: gi|71432656|gb|DR813706.1|DR813706

EST:     TTAATCAACAATAAG                         ATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT
genomic: TTAATCAACAATAAGgttgattcat ... gtgattccagATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT

EST: gi|37384435|gb|CF629288.1|CF629288

EST:     CTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG                         ATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT
genomic: CTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcat ... gtgattccagATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT

EST: gi|5398737|gb|AI812202.1|AI812202

EST:     CTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG                         ATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT
genomic: CTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcat ... gtgattccagATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATT

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: 340

TGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGgttgattcat ... gtgattccagATGCTAAACAAGGAGCACGAGAAGGCCGAGGATTCGAAACCAACCGCCATTCCTACTGCTGCCGGAAGCTAAACGTGCTTTTGATCACTGATTGGTGGCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260