ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgtagccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA

Basic information

species	Zea mays
transcript	GRMZM2G342327_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 4

gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgt--agccactgat-taaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
                                                 |||  || |   |     ||| | | | ||| |||||  |  || |          |||||| ||   | ||||  |    ||   |||||||||||  ||||||||||||| |||||||||||||||||||||||||||||| | |||||||| ||||||||||| ||||| |||||||||||||||||||
--------------------------------------------gtgcgttgcgtactagttagatatttgcatcaattacttatactttgttgcatactagagaactgatgtagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA

upper sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G20130.1 (Glycine max), 3'ss of exon 4

gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgt-agccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
                             ||  |    ||||  |  | |||| |  || |   | | ||   ||||  |  |  || |  |||||| | ||  |   || |||       |    |  | ||   ||||||||  | ||||||||||||||||| || |||||||||||| || ||||||||||||||||||||||| ||||| |||||||||||||||||||||| |
-----------------------------gtatgtttgattttcatta-ttgtgtccttcactatttcttttcttatggatatcaatttattttctcattagatagcaataaaaa-----cttgaatactcat--gcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA

upper sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G08340.1 (Glycine max), 3'ss of exon 5

gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgt-agccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
                             ||  |    ||||  |  | |||| |  || |   | | ||    |||  | |   || |  |||||| | ||| |   || |||      ||    |  |  |   ||||||||  | ||||||||||||||||| || |||||||| ||| || ||||||||||||||||||| ||| ||||| |||||||||||||||| ||||| |
-----------------------------gtatgtttgattttcatta-ttgtgtctttcactatttcttttcctatggattccaatttattttctcattagctagcaatcaaaa-----tttgaatactcgt--gcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA

upper sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G60760.1 (Arabidopsis thaliana), 3'ss of exon 5

gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgtagccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
                                                   ||     | |  ||||| ||     ||||   | || |||||| |   ||       |  || |  |    || | |       ||||||||| | ||||| || |||||||| ||| | || || |||||||||||  |||| ||||| |||||  ||||||||||||| ||  | || |||||||
---------------------------------------------------gtaagactcaatttgttctc-----tttaac-acatttcattt-tgaaagttgtaattctaacttctaacttgtttt-------cagATGGGACTGATGAAAAAGCATCCTTCTATAGTTCCTTTCATGGTATACATCGCAAACGAGGAGAAACATTTGGAACGATTTGCAGTTAGAGCTAAGTACA

upper sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0061g00280.t01 (Vitis vinifera), 3'ss of exon 5

gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgtagccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
                                    || | |  |  ||||  | | ||| | ||   |||   |    ||  || | | | |  |  | |    |  ||| | |  |  |        |||   ||||||||  | |||||||||||||| || || |||||||| ||| ||||||| |||||||| || |||||| |||||||||||||||| ||||||||||| |
--------------------------------gtaagtgtcttcactaatt-ctaattttttttttccttctcctgacaaggaatcttttagtgtt--ttgtttttagttacaatggttgttc-----caattggcagATGGGGCTTATGAAGAAACATCCGTCAATCATACCATTCATGATATACATCACAAATGAAGACAAACACTTGGAACGATTTGCTGTTCGTGCAAAGTATA

upper sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0040g01610.t01 (Vitis vinifera), 3'ss of exon 4

gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgtagccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
                                     |  || | || ||  | ||   ||||               || || | |   |  |  | |||  |   | ||||   ||||| || | | | | | ||||||||  ||||||  ||||||||||| || |||||||| ||| | |||||  ||||||| || |||||  ||||||||||||| || |||||||| ||||
---------------------------------ccttttatttataagatcttctaaactatgc--acaaaaagagaatatttttcttgtaaattgcttagtgat--actaaaaggttctt-tgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA

upper sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S7_501V6.1 (Physcomitrella patens), 3'ss of exon 4

gtacgtat-tagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttat--gttgttttccgttatttagttatatctcatttctcgtagccactgattaaagtcttcttctgctgttaatca--acagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
||| |||| || |    |    |   | || |      |  ||  |||  |  || || |||    ||  |  || ||| ||  ||  || || |   | ||    |  |  |||    |  |  | || ||  |     ||||||  | | |||||||||||||| || || || ||||| ||||| |||||| | || || || ||||||||| || |||||||||| ||||||||  | |
gtaagtatataatttgaagctcggatacggttcc---ttcattgcaaatctgattcagattaccgatttatgccctttagttccttcgatttcttgcgtagtctgtagagggtaatccgtattcttactcttggtttttgcagATGAAACTGATGAAGAAACATCCCTCGATTATTCCATTCATGGTGTACATTGCCAAGGAAGAAAAACACATGCAAAGATTTGCTGTTCGTGCAAAACAGA

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|26558376|gb|CA830611.1|CA830611

EST:     AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTG                         ATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT
genomic: AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTGgtacgtatta ... taatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT

EST: gi|22472504|gb|BU036984.1|BU036984

EST:     AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTG                         ATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT
genomic: AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTGgtacgtatta ... taatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT

EST: gi|32930223|gb|CF035035.1|CF035035

EST:     AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTG                         ATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT
genomic: AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTGgtacgtatta ... taatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT

EST: gi|32934046|gb|CF038858.1|CF038858

EST:     AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTG                         ATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT
genomic: AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTGgtacgtatta ... taatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT

EST: gi|32930712|gb|CF035524.1|CF035524

EST:     AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTNTGTG                         ATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT
genomic: AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTGgtacgtatta ... taatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT

EST: gi|87157272|gb|DY402061.1|DY402061

EST:     AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTG                         ATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT
genomic: AGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTGgtacgtatta ... taatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATT

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: 186

TGAGATGGTGATCGACAGCCTGGACAGGTTAATTACATCCTGGGAAGAGCAGAAAGAATCTGTGATTGTTGAAGGAGTGCATCTAAGCCTTAACTTTGTGgtacgtatta ... taatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 33

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 27

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atatctcatttctcgtagccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA

                                          tgttaat  putative branch site (score: 72)
                               tcttcttctgctgtt  CT-rich tract
                      tgattaaa  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgtagccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG