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

gtgggtctttacttgttcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattgtgggccaattttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC

Basic information

species	Zea mays
transcript	GRMZM2G121826_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G121826_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g61010.1 (Oryza sativa), 3'ss of exon 4

gtgggtctttacttgttcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattgtgggccaattttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC
||| |||  ||| ||| |   |||||  ||| | |   ||  | | | |   || |  | | |  |||||||||  |    ||      ||||| |||||||| ||||| || || || |||||||||||||||||| | ||||| |||||||| ||||| |||||||| ||||||||||||||||| ||||    
gtgagtcagtacctgtgctacttagtaacttct-tagcttgggcttccagtaataaggcatgtaatgttttgatgataaatca------tagGATGGTAACCCCAGACTGTCGTGCTTCGGTCTGATGAAGAACAGCAGGGATGGGAAGAGCTATAGTACCAATTTGGCTTTCACGCCTCCTGAGTACCTTA----

upper sequence: GRMZM2G121826_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4

----gtgggtctttacttg--ttcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattgtgggc--caattttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC
    |||| | ||   |||   | ||  |  ||| | |   ||  ||   || |    |  || |  || || | || || ||   |  ||||||   |||| ||  ||||| | || || |||||||| || |||||||||||| | ||||| || |||||||| || ||| |||| | ||| ||||||||||| |||||   
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTA-CTTAA---

upper sequence: GRMZM2G121826_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S122_66V6.1 (Physcomitrella patens), 3'ss of exon 4

------------------------------------------------------------------------------------gtgggtctttac-ttgttcgcgttagttgcttttct------------gagttttgatacaaagca--ttaaccttt---ttgtgttttgattgtgggccaa---ttttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC
                                                                                      |       || |      || || |  ||||| |              ||||| |   | | |    ||| || |   || |   ||||| ||   |||    |||   |||||||  | ||  | || || |||||||| || ||||||||||| || |||||||| ||||| ||||| ||| |||||| ||| || ||||| || |||||   
gtattgctcttctctgtagcagttttgaactaaaacttggtatgtcccttcccgttcctatcaagtctcgacaatcctgctatacagaacacccacatcaaatacgctaatcacttttttttacggaaaataaggttttaaagtagacctatctaatctgtagattataaattgatggtctcccacgcctttgtcagGAAGGAGATCCGCGCCTCTCTTGTTTTGGCCTCATGAAGAACAGTCGCGATGGAAAAAGCTATAGTACCAATCTGGCCTACACTCCCCCTGAATA-CTTAA---

upper sequence: GRMZM2G121826_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 3'ss of exon 4

----gtgggtctttacttgt--tcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattgtgggcca--attttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC
    |||||| |    | |   | |   || ||  |     || ||    | ||    ||  |    |  || | || |   |   | |  ||||| ||||| ||  ||||| | || || |||||||| || |||||||||||| | |||||||| |||||||| || |||||||| | ||| |||||||||||  | |    
tcgtgtgggtttcctttggaaatagttctacttagtacgtggatttcaactgcagttaatagaatgctcagtatattaacgattctctacgattttgtagGACGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGAAAAAGCTACAGCACCAATTTGGCTTACACTCCTCCTGAGTACTTGA----

upper sequence: GRMZM2G121826_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 3

gtgggtctttacttgttcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattg--tgggccaattttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC
                                  ||  |||| || |    | ||  |||  | |||| |  |||   ||   |  ||||  |||| ||| | ||  | || || ||||| |||||||||||||||||||| || || |||||||| || || || ||||| |  || |||||||| ||  |      
---------------------------------gtgctttttaatccttttcgttc-cctcctagtgtatgcattaactgcagctgttttgcagGACGGTGATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGC----

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|148945740|gb|EC891020.2|EC891020

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCG                         GAAGGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagG----TAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT

EST: gi|71299876|gb|DR785964.1|DR785964

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCG                         GAAGGTAACCCAAGACTATCATGTTTTGGTCTG
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagG----TAACCCAAGACTATCATGTTTTGGTCTG

EST: gi|71772711|gb|DR970638.1|DR970638

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCG                         GAAGGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagG----TAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT

EST: gi|148982427|gb|EE028311.2|EE028311

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCG                         GAAGGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagG----TAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT

EST: gi|149103589|gb|EE288989.2|EE288989

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCG                         GTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAA
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAA

EST: gi|149036971|gb|EE155209.2|EE155209

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCG                         GAAGGTAACCCCAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagG----TAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT

EST: gi|71302365|gb|DR787300.1|DR787300

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCG                         GAAGGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagG----TAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT

EST: gi|9952364|gb|BE638947.1|BE638947

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCG                         GAAGGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagG----TAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT

EST: gi|149012049|gb|EE042465.2|EE042465

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCG                         GAAGGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagG----TAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGAT

EST: gi|9952536|gb|BE639119.1|BE639119

EST:     GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGGAAG                      
genomic: GGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGC----Ggtgggtcttt ... ttatagg

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: 154

GAGGGCTGCATTTTATGTGGCACAGGCGTTGGAATACTGCAGTAGCAAAGGGAGGGCACTCTATCATGACCTGCATGCATACAGGGTCGTCTTCGATGCGgtgggtcttt ... ttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 64

Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 43

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 113

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgatacaaagcattaacctttttgtgttttgattgtgggccaattttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC

                                         aattttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtctttacttgttcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattgtgggccaattttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC

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