ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggttttattagcatgatcatgcatttgggtccacagtctacaactgttacaaaaataatgg...

Basic information

species	Zea mays
transcript	GRMZM5G877597_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 5'ss of exon 3

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTAC-AAAAATCTAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggttttattagcatgatcatg-catttgggtccacagtctacaactgttacaaaaataatgg
 ||||| |||||||||||||| ||||| ||||||||||||||||| || ||||||||||  ||||||||| | |||||  |||| ||| ||||||| |||||||| ||||| |      ||||| |  | |       ||   ||   | | ||||||||| |  ||          | ||  |   ||||     |   ||
-TCTCTCAAACATGAAGATGCAGAGAATATAGGTTATGTGATACCCACCCCAGTTATTATGCATTTCATTCAAGACTATGAAAAGTCTGGAGAATATACAGgtaa-atgctatacaacttaattgcatgaatatgccatttacttctattgtatgatcatggcccttcttcttttcttttagtataattacctctgtttggg

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G09970.1 (Glycine max), 5'ss of exon 3

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgtaatatgctcttttctg--taattactgggagtaattgtt----ggttttattagcatgatcatgcatttggg--tccacagtctacaac---tgttacaaaaataatgg----
 || || || ||||||||||||||||| ||||||||||| || || || |||||||| |  ||||| ||  |||| ||  | ||   | ||| ||| || ||||||||| |   | |    |||    | |   | | | ||    | |  ||| ||     |  |  | |||    |  |    ||   |    | || |  ||      |    
-TCCCTCAAGCATGAAGATGCGGAGAATATAGGTTATGTCATTCCAACGCCAGTTATCATGCATTTTATCCAGGATTATGAGAAGAATGGAGGATATACTGgtaatatggtagctacaaactaagatgtagatttcacttttacaagatgctatcagagcatttttagaattgaagttttatgcactgagatctttctttctcaatctgctgttag

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G16820.1 (Glycine max), 5'ss of exon 3

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgta----atatgctcttttctgtaattactgggagta-attgttggttttattagcatgatcatgcatttgggtccacagtctacaactgttacaaaaataatgg
 ||||||||||||||||||| |||||| ||||| ||||| ||||| || ||||||||   |||||| ||    |||||  ||||   | | | ||| |||||||    | | | | ||||   |  ||         | |   ||    ||  ||        || |||||       |    |    ||  |  | |   |||  
-TCTCTTAAACATGAAGATGTGGAGAATATAGGATATGTAATACCCACCCCAGTTATCCTACATTTTATCCGAGACTATGAAAAGAATGGGGCATATACAGgtatctaaaaggatgttttacttctttgtctatttcatacccttctccttcctaaagaagatat-catttactcttgct-cttgtgtctact-tagaggaaat--

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G01930.1 (Glycine max), 5'ss of exon 3

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggttttattag------catgatcat-----gcatttgggtccacagtctacaactgttacaaaaataatgg-------
 || || || ||||||||||||||||| ||||||||||| || || || |||||||| |  ||||| ||  |||| ||  | ||   | ||| ||| || ||||||||| |   |   | || ||   |  |||  | |   |||||  ||      | ||| |||     | |||  | |  |    ||   |   ||       ||   |       
-TCCCTCAAGCATGAAGATGCGGAGAATATAGGTTATGTCATTCCAACGCCAGTTATCATGCATTTTATCCAGGATTATGAGAAGAATGGAGGATATACTGgtaatatggtagcta--ggaacta--agatgtagatttcacttttacaagatgctacctgagcatttttagaattaagttttatgcactcagatctttctttctctatctgctgttag

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv17s0000g07900.t01 (Vitis vinifera), 5'ss of exon 3

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggttttattagcatgatcatgcatttgggtccacagtctacaactgttacaaaaataatgg----
 |||||||||||||||||||| ||||| ||||||||||| ||||| || ||||| || |  || || ||  | || ||  | ||   | ||| ||| || |||| | |  |   || ||   | |          ||| |  | || ||       |  || |     |   ||||| ||    |||    ||  |  |      
-TCTCTTAAACATGAAGATGCAGAGAATATAGGTTATGTCATACCAACACCAGTCATCAAGCACTTTATCCAAGATTATGAGAAGAATGGAGCATATACTGgta-tgtatttgattgtggcttcaactatttcggttgataatgttcttgttggatttttgaac---agcttacagtttatctttgtgcataacttccttatgat

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv14s0066g01660.t01 (Vitis vinifera), 5'ss of exon 3

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggtttta-ttagcatga-tcatgcatttgggtccacagtctacaactgttacaaaaataatgg
 || ||||||||||||||||  ||||| ||||||||||| ||||| || ||||||||||  || |||||   ||| ||  | ||   | | | ||| ||||||         | |  | |  |   |   |||   |||  ||||||  |  || || | |  |  ||      |   |||| |  ||||       |     
-TCCCTTAAACATGAAGATGTAGAGAATATAGGTTATGTCATACCAACGCCAGTTATTATGCACTTCATCCGGGATTATGAGAAGAATGGTGCATATACAGgtgcatcagagtgtagtcttgtgcttttcagtttgtgtctgttttaactctcacgagttactctctttatataattatctaaatgtgttcttg--ttggcta

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|91054928|gb|EB165346.1|EB165346

EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

EST: gi|78090489|gb|DV518863.1|DV518863

EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

EST: gi|91054929|gb|EB165347.1|EB165347

EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

EST: gi|94472958|gb|EB701916.1|EB701916

EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

EST: gi|71431610|gb|DR812660.1|DR812660

EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

EST: gi|78084750|gb|DV513143.1|DV513143

EST:     AAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: AAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

EST: gi|71311298|gb|DR791964.1|DR791964

EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

EST: gi|74246237|gb|DT654151.1|DT654151

EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

EST: gi|88748255|gb|DY532396.1|DY532396

EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACGGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

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), 46 (downstream exon)
Score: 25

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCTCTCAATGGTGTTGGTCTTTGTCCTGCTAGTAGATCACTTAGCACCCATG

Block sizes: 41 (upstream exon), 44 (downstream exon)
Score: 18

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 24