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

...gataaatggagagaaaataatgatgtcgagtgagctattctggtaactcgttgaacatagccataagtgtaatttgtattatcatttctttcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA

Basic information

species	Zea mays
transcript	AC215690.3_FGT002
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC215690.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g31070.1 (Oryza sativa), 3'ss of exon 2

gataaatggagagaaaataatgatgtcgagtgagctattctggtaactcgttgaacat-agccataagtgtaatttgtattatcatttctttcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA
  | | || |    | |       || |  || | |||||    |     || |   | |||||  | | ||||||    | |  |  ||  ||| |||||||||| ||||||||||| || ||||||||||||||||| ||||||||||| |||||||| || |||||| | || ||||| |||||||||||||| ||||
attcactgcattttagaatcaaccgtggtatg-gttattcataaattaatttcattgttagccacgaatctaatttcacctcttgtacctaccttctgcagGATCCAGGAACTGAGAATAATCCCTACTTGGGTTTCCTTTACACATCATTTCAAGAAAGAGCTACATTTATATCCCATGGCAATACTGCAAGGCACGCCA

upper sequence: AC215690.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: PP1S146_17V6.3 (Physcomitrella patens), 3'ss of exon 3

-gataaatggagagaaaataatgatgtcgagtgagctattctggtaactcgttg-aacatagccataagtgtaatttgtattatcatttctttcttat-gcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA
  || ||   |   | |||| |   ||||  |     ||  | | ||    | | ||      | |     | | ||| ||  |  ||||| |   || |||||| |||  ||| |||||||| ||||||||||||||| | ||||| || ||||| ||||||||||||||  | || ||||| || |||||  |||| ||||
taatgaaaaaaactagaatagttg-gtcgcattt-tcatcttagaaatgactcgcaattctatcctgcccatcaattg-atcgttgtttctgtgcgattgcagGACCCTCAAACAGAGAACAATCCCTACTTGGGTTTCGTTTACACCTCCTTCCAGGAAAGGGCAACATTCATTTCACATGGTAACACTGCTCGGCACGCCA

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|32847096|gb|CD986777.1|CD986777

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|74245141|gb|DT653055.1|DT653055

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|93281940|gb|EB674204.1|EB674204

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|18964949|gb|BM661303.1|BM661303

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCC

EST: gi|60352849|gb|DN219822.1|DN219822

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|18964947|gb|BM661302.1|BM661302

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCC

EST: gi|32844409|gb|CD984090.1|CD984090

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|74244362|gb|DT652276.1|DT652276

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|32833577|gb|CD973255.1|CD973255

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|32846330|gb|CD986011.1|CD986011

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|32845620|gb|CD985301.1|CD985301

EST:     ACATGAAACAAATTGAGAAGACCATCCAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|18964155|gb|BM660842.1|BM660842

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGNTCCGGAATG                         GATCCTGGAACTGAGAACAACCCC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCC

EST: gi|22542531|gb|BU092969.1|BU092969

EST:     ACATGAAACAAATTGAGAAGACCATACAACATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

EST: gi|6626396|gb|AW257928.1|AW257928

EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGNGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

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: 48 (upstream exon), 49 (downstream exon)
Score: 457

CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 649

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 584

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1451

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

actcgttgaacatagccataagtgtaatttgtattatcatttctttcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA

 tggtaac  putative branch site (score: 1451)
                                 ttatcatttctttctt  putative PPT
                        taatttgtattatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataaatggagagaaaataatgatgtcgagtgagctattctggtaactcgttgaacatagccataagtgtaatttgtattatcatttctttcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - -ttctggt
- - - - - - - - - - - - - - - - - - - - - - - - - - gaacata