ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggttggttctttatttgtgtttgtgcagatgtctttcataggtttctattacatttgcaaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag

Basic information

species	Zea mays
transcript	GRMZM2G039325_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 4

TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagt-cttttatggttggttctttat--ttgtgtttgtgcagatgtctttcataggtttctattacatttgc-aaatattttacgcctccagtcaccct---cgatgatctaattaccct------tttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatc--ttgttttcag
|||||||||||||||||||||||| || |||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||| |||| || ||||| | |||| || |    ||      || | |||  || ||||||||  | |   |||| || | ||   | ||| || |  | ||||||   ||||  ||   |||   ||   |  || || || |      ||| || |   |  ||||||| ||  |    ||    ||||| |||||| |   ||   || ||
TTTGCGGAGAGTACATGCAGCCCAAAAGGATGATGACATGCCACCAATTGAAGCCATTCTCGCACCGCTTGAAGCTGAGCTAAAGCTTGCTCGGCAAGAGgtgaaactttgttcacccatcccccattttctatcattttgtttgtgtggtttaatttcttatgctttcctaacagttactgattattttcatcctctggtttgcctaaacggctaattagttgccttagtttcttttcattggtttgtgtattttctatgatcaaataagatgaccagttaacttggttcactttag

upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4

TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggttggttctttatttgtgtttgtgcagatgtctttcataggtttctattacatttgcaaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag
| | || || || || || ||||||||||||||||||||||| ||||| ||||| |||||||| ||  | |||||||| || |||||| |||| || |||||| ||| | || | ||   |||  |  | || |    |      |||  |  |  |  |  ||  | |   ||   ||||   | |    |  | |    ||      || | |||  | || |                                                          
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgt-tcttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggctt--aaaatgagtaattttttgatttgtact------tccatttattccttgcag--------------------------------------------------------

upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G26540.1 (Glycine max), 5'ss of exon 4

TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggttggttctttatttgtgtttgtgcagatgtctttcataggtttctattacatttgcaaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag
| |  | || || ||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||  | |||||||| || |||||| |||| || |||||| ||| | || | ||   |||  |  | || |     | | | |   |   ||   |||  |  |      ||  ||||   |      |    |    ||      || | |||  | || |                                                          
TCTTAGAAGGGTCCATGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCACCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgt-tcttggagttcatattataatc-ccctggagaaagagctgttggaaggactgaaactggctta-aaatgagtggttttttactttgtact------tccatttattccttgcag--------------------------------------------------------

upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4

TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggtt-ggttctttatttgtgtttgtgcagatgtctttcataggtttctattacatttgcaaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag
 ||  | || || ||||| || || || |||||||| ||||| || |||||||||||||| || ||| | ||||||||||| |||||  |||||   ||||||    ||| || |||   ||     | | || |||    |  | | ||   |||   | |||||| | |                                                                                                                 
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtatgttttactcatttgaagtccaaatttctacttgcaaat-cggatattaatttatgatgtttctgtgaag---------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 4

TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggttggttctttatt-tgtgtttgtgcagatgtctttcataggtttctattacatttg-caaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag
|||  | ||||| ||||| || || || |||||||||||||| || ||||||||||| ||||| ||| | |||||||| || |||||| | ||    |||||| || ||    ||||| |  |   |  ||  | | |  ||    |   |   || | || ||   |   || |   ||||| | ||    ||   ||                                                                                      
TTTAAGAAGAGTCCATGCTGCTCAAAAGGATGATGACATGCCTCCTATTGAAGCCATCCTTGCTCCATTAGAAGCTGAACTTAAGCTTGCACGATCAGAGgta-ta-ttgtcattttaagtctaactgcttgctgtttactttcatatgggatattgaaagtttatgaggtcactgatcaaatctcttgtatctgt-gtag------------------------------------------------------------------------------------

upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 5'ss of exon 4

TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggttggttctttatttgtgtttgtgcagatgtctttcataggtttctattacatttgcaaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag
| | || || || ||||| || || || |||||||||||||| ||||||||||| |||||||| ||  | |||||||| || || |||||  | || || |||        | ||   |  || |  |   | ||   |||||  || |    ||||     ||     ||||||   || |  ||    |||   |     |  ||| | | |||                                                                   
TCTTCGTAGGGTTCATGCTGCTCAAAAGGATGATGACATGCCTCCAATTGAAGCTATTCTTGCCCCTTTAGAAGCTGAACTGAAACTTTCGAGACAAGAAgta--------ttttccttcctttgaaccagaattacctttgtatagct-cgattcaacaacttacgggacattt---aacagctt---tctcatatgggtttacatgttttgattggtag--------------------------------------------------------------

upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 4

TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggttggttctttatttgtgtttgtgcagatgtctttcataggtttctattacatttgcaaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag
| |  | || || ||||| || ||||| ||||| || ||||| || |||||||| |||||||||||  | || |||||||| |||||| |||| ||||||||| |      | ||  |||  |||   || |  |   ||  ||  ||| ||||||  |   |   | | |  |   | ||  |  |         |     |   ||     |||     ||| ||                                                        
TCTTAGAAGGGTTCATGCTGCGCAGAAGGATGACGATATGCCTCCCATTGAAGCGATTCTTGCACCGTTGGAGGCTGAGCTCAAGCTTGCTCGGCAGGAGgtagt------tattgcatg--tggcctttaaactt--ttaatgacgat-tctttctcaaagtaaaactcc--tcatagatgataaatagtagttatatgattgtttggctgtattggttcttttcag-------------------------------------------------------

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|149084677|gb|EE174161.2|EE174161

EST:     AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAG                         ATTGCAAATCTCCAGGATGANCA-CAGAGCTTTGGAT
genomic: AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatactta ... ttgttttcagATTGCAAATCTCCAGGATGA-CAACAGAGCTTTGGAT

EST: gi|32931881|gb|CF036693.1|CF036693

EST:     AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAG                         ATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA
genomic: AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatactta ... ttgttttcagATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA

EST: gi|71444483|gb|DR825533.1|DR825533

EST:     AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAG                         ATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA
genomic: AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatactta ... ttgttttcagATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA

EST: gi|13381901|gb|BG458576.1|BG458576

EST:     AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAG                         ATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACATATCTT
genomic: AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatactta ... ttgttttcagATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA

EST: gi|148943243|gb|EC888304.2|EC888304

EST:     AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAG                         ATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA
genomic: AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatactta ... ttgttttcagATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA

EST: gi|148967769|gb|EE019046.2|EE019046

EST:     AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAG                         ATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA
genomic: AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatactta ... ttgttttcagATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA

EST: gi|76930993|gb|DV172583.1|DV172583

EST:     AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAG                         ATTGCAAATCTCCAGGAT
genomic: AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatactta ... ttgttttcagATTGCAAATCTCCAGGAT

EST: gi|71439208|gb|DR820258.1|DR820258

EST:     AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAG                         ATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA
genomic: AAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatactta ... ttgttttcagATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAA

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: 257

TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatactta ... ttgttttcagATTGCAAATCTCCAGGATGACAACAGAGCTTTGGATCGTCTAACAAAACAAAAGGAGGCAGCTCTGCTAGAAGCAGAGAGGACTGTGCAAATTGCTATGG

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 82

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 73

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 142

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggttggttctttatttgtgtttgtgcagatgtctttcataggtttctattacatttgcaaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA