ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacacacctttctgtcttatggaatagaggttggaacttgtaattaatcagtaaggtctgttctatttcgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G127591_T03
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G127591_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g59550.1 (Oryza sativa), 5'ss of exon 4

TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtac-tacacacctttctgt---cttatggaatagaggttggaacttgtaattaatcagtaaggtctgttctatttcgtgcag-------------------------------------------------------------------------
||||||| || ||||||||||||||||||||||||||||| ||||| ||||| |||||||| ||||||||||| |||||||| |||||||| |||||||||||  | | || |||   |      ||  || | | | ||      ||   | |      |       | || | | ||  |                                                                          
TCAACATGTTTGGTTTCTGTGCTGCCATGGTTGGCTGCCTTGCTACATCTACCAAGACCATTTTGGCAGAGTCTCTACTCCACGGATACAAATTTGACAGgtaggtgctcatcttatggcgggtgtaatgactggtgctttacttctgctgtgatcttacagttataatactgtatggtaaactggatttttttgtcgccgtgttaccagcaaagtaaatcatgttatttatgacgtttccttgtgttttcttcag

upper sequence: GRMZM2G127591_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G42900.1 (Glycine max), 5'ss of exon 3

TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacacacctttctgtcttatggaatagaggttggaacttgtaattaatcagtaaggtctgttctatttcgtgcag-------------------------
| || || || || |||||||||||| |  |||||||  ||||||| ||||||||||| ||  | ||||| || || || ||||||||||| ||||||||||||       |||| | | |  | | ||     |||    |  ||| |    | |  ||| |  | | |||| |                             
TTAATATGTTTGGATTCTGTGCTGCCTTATTTGGCTGTTTGGCTACATCTACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtacggt----ctttatttatggttgcattccctttgctgttattaacttggtattttggtgttctttttttcctttctccatttttttgtctttctggatttt

upper sequence: GRMZM2G127591_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G23570.1 (Glycine max), 5'ss of exon 3

TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacacacctttctgtcttatggaatagaggttggaacttgtaattaatcagtaaggtctgttctatttcgtgcag--------------------------
| ||    || || || ||||||||| |  | |||||  ||||||| ||||||||||| ||| | |||||||| ||  | ||||||||||| |||||||||| | | ||   ||| || |||      |     |||| | ||||| |  ||  |  ||||   |  || |   |                              
TTAATGCATTTGGGTTTTGTGCTGCCTTATTGGGCTGTTTGGCTACATCTACAAAGACTATCCTTGCAGAGTCTCTGTTGCATGGATACAAATTTGACAGgtgc-aaac-tttttatgccttgcc---ttctttttggtatttgtagtccatttgacaggtgcatgttagtcaatattttctggaatttataaaaaattgttagc

upper sequence: GRMZM2G127591_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G03210.1 (Glycine max), 5'ss of exon 4

TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacacacctttctgtcttatggaatagaggttggaacttgtaattaa------tcagt-aaggtctgttc---tatttcgtgcag-------------
| ||    || || || ||||||||| |  |||||||  ||||||| ||||||||||| ||| | |||||||| ||  | ||||||||||| ||||| |||| | | ||   ||| || ||||   ||||     ||||  || |||  ||      | ||| ||  | | |     | |||| | ||              
TTAATGCATTTGGGTTTTGTGCTGCCTTACTTGGCTGTTTGGCTACATCTACAAAGACTATCCTTGCAGAGTCTCTGTTGCATGGATACAAATTTGATAGgtgc-aaac-tttttatgccttagtcaatattttctggattttataaaaaaaaaatgttagtcaatatttatatacatttttcattcaaacaccttaaagtc

upper sequence: GRMZM2G127591_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G11850.1 (Glycine max), 5'ss of exon 3

TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacacacctttctg--tcttatggaatagaggttggaacttgta-attaatcagtaaggtctgttctatttcgtgcag------------------
| || || || || |||||||||||| |  |||||||  ||||||| ||||||||||| ||  | ||||| || || || ||||||||||| |||||||||||| |      ||| ||  ||   |    | |  |||   |  | |  |||  |   |    | | | |  |||   |                     
TTAATATGTTTGGATTCTGTGCTGCCTTATTTGGCTGTTTGGCTACATCTACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctttttttatggttccattccctttgttgttattatctttgtatttctttttttcctttctccattttttcgtctttctggacttcccagtag

upper sequence: GRMZM2G127591_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT1G21870.1 (Arabidopsis thaliana), 5'ss of exon 3

TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgt-actacacacctttctgtcttatggaatagaggttggaacttgtaattaatcagtaag-gtctgttctatttcgtgcag-----------------------------------------------------------------------------------------------------
| ||  | || || |||||||||||  || |||| ||  | ||||| ||||||||||||||  | ||||| || || || ||||||||||| |||||||||| | |   |   || |||   | | ||      |||  |  |  ||  |  | | |  | |    ||  |||| ||                                                                                                         
TTAATGTGTTTGGATTCTGTGCTGCTTTGTTTGGATGTTTAGCTACCTCTACAAAGACCATTCTTGCAGAATCTCTTCTTCATGGATACAAATTTGACAGgtcaatgttctgtttcctgaggttttgatcttcagtttcacatgataggtgttgaatgtgtgaaacttacatttggtttcaatgacatgccatgctctcatagtccaatacttgatttgctttttcatatttcatggaactgagtgtttgtgtcctcctcattttcatgtctctctatgtag

upper sequence: GRMZM2G127591_T03 (Zea mays), 5'ss of exon 4
lower sequence: PP1S60_175V6.2 (Physcomitrella patens), 5'ss of exon 5

TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtact---------acacacctttctgtcttatggaa--tagaggttggaacttgtaattaatcagtaaggtctgttctatttcgtgcag-----------------------------------------------------------------------
|||| ||    ||||||   || ||  |  |||||||| | |  || || |||||||||||||||||||| ||| | || ||||| ||||| ||||| ||||| |         ||||  ||  ||||  |  | ||   ||| |    | |    ||||  ||   ||  |       ||   |||||                                                                        
TCAATATGGCTGGTTTCCTAGCAGCTTTTTTTGGCTGCGTCGTGACTTCGACAAAGACCATCTTGGCAGAATCCTTGCTTCATGGTTACAATTTTGATAGgtattttgatttcaacactactagctgtactcagtaagtcagaaggcttaccactgaatttttcttcaatctaccagagatcatgtgcataattagagttctactgaacttttcctctgcaattttaggtttgacaactgatgcgttaacctctaatgcag

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|21843199|gb|BQ703780.1|BQ703780

EST:     ACAAAGACCATCTTGGCAGAGTCCCTGCTCCATGGATACAAGTTTGACAG                         CATTAACACGGNGTACTACATGGCACCCTTTGNCACCATGATACTGGCTCT
genomic: ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|149099201|gb|EE185229.2|EE185229

EST:     ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|56382297|gb|CV984966.1|CV984966

EST:     GTCCCTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: GTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|76289586|gb|DV029154.1|DV029154

EST:     ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|50328830|gb|CO523956.1|CO523956

EST:     CATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: CATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|18166348|gb|BM336187.1|BM336187

EST:     AAAGACCATCTTGGCAGAGTCCGTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: AAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|22520681|gb|BU079492.1|BU079492

EST:     ACAAAGACCATCTTGGCAGAGTCCCTGCTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|13149872|gb|BG320194.1|BG320194

EST:     ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|211018876|gb|FL463754.1|FL463754

EST:     CCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTATGACAG                         CATCAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: CCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|60351094|gb|DN218067.1|DN218067

EST:     ATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: ATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|76909994|gb|DV163641.1|DV163641

EST:     ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|24768736|gb|CA403865.1|CA403865

EST:     ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

EST: gi|17931203|gb|BM268163.1|BM268163

EST:     ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAG                         CATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT
genomic: ACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCT

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: 197

TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacaca ... tttcgtgcagCATTAACACGGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCTACCAGCGATGGTGCTTGAAGGAGGAGGTGTAATGAACTGGTTCTACACA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACATTTTCGGTTTCTGTGCTGCCATGGTTGGCTGCCTGGCTACGTCTACAAAGACCATCTTGGCAGAGTCCCTACTCCATGGATACAAGTTTGACAGgtactacacacctttctgtcttatggaatagaggttggaacttgtaattaatcagtaaggtctgttctatttcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA