ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGTAAATTTGTTGACATCGACCATTAAAGTTGATGCTGAGCAATCAGATTTGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgtatagcacaagtttatggtctgtcatattgaatatgatcaagacttccatacttcatgaacatatctgctatttatacag

Basic information

species	Zea mays
transcript	GRMZM5G872204_T02
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G872204_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA08G28890.2 (Glycine max), 5'ss of exon 13

TGTAAATTTGTTGACATCGACCATTAAAGTTGATGCTGAGCAATCAGATTTGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgt-atagcacaagtt-tatggtctgtcatattgaatatgatcaagacttccata-cttcatgaacatatctgctatttatacag----------
||| || ||| | ||||| || |||||||| |||||||| ||||||||||||||||| || ||| | || |||||||| || |||| ||| || |||||||| ||   |   ||| | | |  | |  || |  |||     | |      | | ||| ||      ||    || |||| |            
TGTGAACTTGCTTACATCAACAATTAAAGTAGATGCTGACCAATCAGATTTGAGGTTTTGCTTCCGGATCATTTCACCAACCAAGAACTATACTTTGCAGgttatttaatgtgttctttagatttttttaattcatacatggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcag

upper sequence: GRMZM5G872204_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA18G51810.1 (Glycine max), 5'ss of exon 13

TGTAAATTTGTTGACATCGACCATTAAAGTTGATGCTGAGCAATCAGATTTGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgt-atagcacaagtttatggtctgtcatattgaatatgatcaagacttccat----acttcatgaacatatctgctatttatacag----------
||| || ||| | ||||| || |||||||| |||||||| ||||||||||||||||| || ||| | || |||||||| ||||||| |||||| |||||||| ||   |   |||| | |  | |  | || | |   |  | ||     ||     ||| ||      ||    || |||| |            
TGTGAACTTGCTTACATCAACAATTAAAGTAGATGCTGACCAATCAGATTTGAGGTTTTGCTTCCGGATCATTTCACCTACAAAGAACTACACTTTGCAGgttatttaatgtgttttttggatttttttttaattcatacaaggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcag

upper sequence: GRMZM5G872204_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA04G37780.1 (Glycine max), 5'ss of exon 13

TGTAAATTTGTTGACATCGACCATTAAAGTTGATGCTGAGCAATCAGATTTGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgtat------agcacaagtttatggtctgtcatattgaatatgatcaagacttccatacttcatgaacatatctgctatttatacag
 || ||  || | ||||| || || ||  |||||||||| || |||||||| |||||||| ||||| |||||||||||  ||||||  || ||||||||||||       |  | ||  |  ||    ||  | | | || | ||||  ||| |  |   || | |  |   |    ||  || |||
AGTGAACCTGCTCACATCAACAATCAAGATTGATGCTGAACAGTCAGATTTAAGGTTCTGCTTCAGGATTATTTCACCATCAAAGAGTTATACATTGCAGgtactcattcaaaaaaatctagtgacacgtactttggcattttatcattactcctctgtctcctcactaaggccaaaata-atgcag

upper sequence: GRMZM5G872204_T02 (Zea mays), 5'ss of exon 13
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 5'ss of exon 13

TGTAAATTTGTTGACATCGACCATTAAAGTTGATGCTGAGCAATCAGATTTGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgtatagcacaagtttatggtctgtcatattgaatatgatcaagacttcca----tacttcatgaacatatctgctatttatacag--------------------------------------------------------------------------------------------------------
 || ||  |||||||||| || || || ||||||||||| || |||||| | ||||| |||||||| |||||||| || || |||| ||| || ||||||||| | |  |    |  |||    |  ||  | |    |  |    |       || || ||      | ||| ||||| | |                                                                                                          
AGTGAACCTGTTGACATCAACAATAAAGGTTGATGCTGATCAGTCAGATCTCAGGTTTTGTTTCAGGATTATTTCTCCAACGAAGAACTATACTTTGCAGgtaaatcttacagcttaggttgcactcatgaagttcagtttacttctttgaaattatttgatacctgaaactg-tatttttgcttgatggttctgtgaaatactgatggaatggtgaattgttaagtgttattattgatttttttctcactagtgctcattaatgttgtacatttgcttgtcagcacag

upper sequence: GRMZM5G872204_T02 (Zea mays), 5'ss of exon 13
lower sequence: Vv17s0000g00310.t01 (Vitis vinifera), 5'ss of exon 13

TGTAAATTTGTTGACATCGACCATTAAAGTTGATGCTGAGCAATCAGATTTGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgtatagca-caagtttatggtctgtcatattgaatatgatcaagacttccatacttcatgaacatatctgctatttatacag------------------------------------------------------------------------------------------------
||| || ||  ||||| | || || ||  ||||||| || || ||||||||||||||||| ||||| || |||||||| ||||||| ||| || ||||||||| |  | |||   |  | ||    ||||  | |  | |    | |  |||  ||   ||  |||  |          |||                                                                                                
TGTGAACTTACTGACAGCAACAATAAAGCTTGATGCAGATCAGTCAGATTTGAGGTTCTGCTTCAGGATCATTTCACCAACAAAGAACTATACTTTGCAGgtacaaaatcaaaggttagatcaaaaatataaatttgggttttcatt--catgtttttagactatacttatatgaagctcagcattatcagcccaaatacttgtccagtactaatgctggggattatgtcagtacctagagcagattctctcaactttatattaacacttgaatgcag

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|71439574|gb|DR820624.1|DR820624

EST:     TGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAG                         GCAGAGAGTGCAGTATATCAGATGGACTGGATTGAAAAGATAACTGGTGTT
genomic: TGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgtatagcaca ... atttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTT

EST: gi|71439575|gb|DR820625.1|DR820625

EST:     TGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAG                         GCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTT
genomic: TGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgtatagcaca ... atttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTT

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: 45 (upstream exon), 45 (downstream exon)
Score: 101

TGTAAATTTGTTGACATCGACCATTAAAGTTGATGCTGAGCAATCAGATTTGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgtatagcaca ... atttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG

Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 25

Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 16