ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CACTCGGTTGAGCATTACACCCAGGTCAAGCTCAAGAAGCGTGGCTCGGACACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatcactagactcgcctcattttaacctgtgaaatattgacataccttgtactgtgagctagttgtagttgtacttgcaatgagctaaactttgt...

Basic information

species	Zea mays
transcript	GRMZM2G165969_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G165969_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 5'ss of exon 1

CACTCGGTTGAGCATTACACCCAGGTCAAGCTCAAGAAGCGTGGCTCGGACACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatcact-agactcgcctcattttaacctgtgaaatattgacataccttgtactgt-gagctagttgtagttgtacttgcaatgagctaaactttgt--
||||| || ||||| ||||||||||||||||| |||||| | || ||||| ||||| |||||||| || || || || || |||||||||||||||||||||||| ||  |  | |||||    | ||||  ||  | | ||| |||     ||   |  | |   |  ||| | |  |   |  |||| || |     |||  
CACTCCGTCGAGCACTACACCCAGGTCAAGCTTAAGAAGAGGGGATCGGATACCAAATACCTTGCCACCGTTCTCGCTATTGGCACCGAGTGTGACATTGgtatgtatagcccacactcgtgcgacttta--cta-ggactatggactagtttttggcaatcggaatccttgcaatgtttggtaaaatg-gcaatgtcctgtga

upper sequence: GRMZM2G165969_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G09970.1 (Glycine max), 5'ss of exon 1

CACTCGGTTGAGCATTACACCCAGGTCAAGCTCAAGAAGCGTGGCTCGGACACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgta-tgcatcactagactcgcctcattttaacctgtgaaatattgacataccttgtactgtgagctagt--tgtagttgtacttg-caatga-gctaaactttgt
|| || || || || ||||| ||||||||||||||||| ||||| || || ||||||||| | || ||||| || ||||| || ||||| ||||| |||||||    |  ||||    |   ||||||       |  ||| || | | | |  | |  |     |||   |||||    |   | |||| | | | ||      
CATTCCGTGGAACACTACACGCAGGTCAAGCTCAAGAAACGTGGTTCTGATACCAAGTACTTGGCCACTGTGCTCGCCATTGGAACCGAATGTGATATTGgtaacaaacaactaactccttgtcatttatttactttgaat-ttcatacaacgagaatagatgtatagaaatgtagaatcataagacaataacggtgaata----

upper sequence: GRMZM2G165969_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G01930.1 (Glycine max), 5'ss of exon 1

CACTCGGTTGAGCATTACACCCAGGTCAAGCTCAAGAAGCGTGGCTCGGACACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatcactagactcgcctcattttaacctgtgaaatattgacataccttgtactgtgagctagttgtagttgtacttg-caatgagctaaactttgt-
|| ||||| || || || || ||||||||||||||||| |||||||| || ||||||||| | || ||||| || ||||| || ||||| |||||||||||||  || |  |   || | |   | || || | |||| |    |||    |  ||  ||     |  | |||    | | | |||| |     | |  || 
CATTCGGTAGAACACTATACACAGGTCAAGCTCAAGAAACGTGGCTCTGATACCAAGTACTTGGCCACTGTGCTCGCCATTGGAACCGAATGTGACATTGgta-acaactatctccttgtcatttatttactt-tgaatttaatacaaggatgatagagtagtagaaatttagaatcattagacaataacagtgaataagtg

upper sequence: GRMZM2G165969_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G16820.1 (Glycine max), 5'ss of exon 1

CACTCGGTTGAGCATTACACCCAGGTCAAGCTCAAGAAGCGTGGCTCGGACACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatcactagactcgcctcattttaacctgtgaaatatt-gacataccttgtactgtgagctagttgtagttgt-acttgcaatgagctaaactttgt---
|| || ||||||||| |||| || ||||| |||||||| || ||||| || ||||| ||| | || || ||||| ||||| || ||||||||||| || |||||        |   || | | || ||| |||     || || |  ||    | ||        || || | ||| | | ||    ||       |||| |   
CATTCTGTTGAGCATCACACACAAGTCAAACTCAAGAAACGCGGCTCTGATACCAAATACTTGGCCACCGTCCTCGCCATCGGGACCGAGTGTGATATCGgtattt-----caatttcactttatattatccttcttcattttagggatggaatttatgagacagtactttttgttcttaattattttgttggtgcctttctatc

upper sequence: GRMZM2G165969_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1

CACTCGGTTGAGCATTACACCCAGGTCAAGCTCAAGAAGCGTGGCTCGGACACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatcactagactcgcctcattttaacctgtgaaatattgacataccttgtactgtgagctagttgtagttgtacttgcaatgagctaaactttgt
|||||||| |||||| |||| ||||| ||| |||||||||| |||||||||||||||||||| || |  || |||||||| || ||||||||||||||||||  |  ||       |       |||    ||      | ||  | | | |||| || | ||                                     
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtttccaagcttttatggtgtttatgacttctttttgtttgctt-ctttgttctatcag-------------------------------------

upper sequence: GRMZM2G165969_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ16073 (Selaginella moellendorffii), 5'ss of exon 1

CACTCGGTTGAGCATTACACCCAGGTCAAGCTCAAGAAGCGTGGCTCGGACACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatcactagactcgcctcattttaacctgtgaaatattgacataccttgtactgtgagctagttgtagttgtacttgcaatgagctaaactttgt
|||||||| |||||| |||| ||||| ||| |||||||||| ||||||||||||||||| || || |  || |||||||| || ||||||||||||||||||  |  ||       |       ||     ||      | ||    | | |||| || | ||                                     
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTATCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtttccaagcttttatggtgttcatgacttctttttgtttg-gttctttgttctatcag-------------------------------------

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|148999303|gb|EE036236.2|EE036236

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG

EST: gi|71318779|gb|DR796146.1|DR796146

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG

EST: gi|149086117|gb|EE175658.2|EE175658

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG

EST: gi|71328704|gb|DR801033.1|DR801033

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG

EST: gi|149105907|gb|EE291527.2|EE291527

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCT
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCT

EST: gi|148948629|gb|EC898541.2|EC898541

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG

EST: gi|74232980|gb|DT640894.1|DT640894

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG

EST: gi|149083010|gb|EE172257.2|EE172257

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG

EST: gi|78116159|gb|DV534547.1|DV534547

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGATTTCTGGAAAGGCGTTTCACCTGTAG
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG

EST: gi|31364573|gb|CD448928.1|CD448928

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAG

EST: gi|211026683|gb|FL134293.1|FL134293

EST:     ACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTTG                         CAATGT-GACCGTTGAAGATGATGAATTNCTGGAAAGGCGTTTCACCTGT
genomic: ACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATT-Ggtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATT-CTGGAAAGGCGTTTCACCTGT

EST: gi|74243585|gb|DT651499.1|DT651499

EST:     CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTG                         CAATGTTGACCGTTGAAGATGATGAATTCTGGAAAG-CGGTTTCAC-TGTA
genomic: CACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCG-TTTCACCTGTA

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: 42 (upstream exon), 49 (downstream exon)
Score: 119

CACTCGGTTGAGCATTACACCCAGGTCAAGCTCAAGAAGCGTGGCTCGGACACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatca ... ccgttttcagCAATGTTGACCGTTGAGGATGATGAATTCTGGAAAGGCGTTTCACCTGTAGAGTTTGGGTCGCTGCCAGCACTTCAGGATGCCGTCACTGTTGTTGGTTA

Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 52

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65