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

...ggcgtaagtaaggatcagtctagaggtttggttgccaagttcagtgcactacgctgacactccctcctctccctgcgtgcactgctgctagtaccagcagCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGACCCACCTGTTCGTGCCGGGCCCCGTGAACATCCCGGACCCCGTGATCCG

Basic information

species	Zea mays
transcript	GRMZM2G137868_T04
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G137868_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g39300.2 (Oryza sativa), 3'ss of exon 1

-ggcgtaagtaaggatcagtctagaggtttggttgccaagttcagtgcactacgctgacactccctcctctccctgcgtgcactgctgctagtaccagcagCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGACCCACCTGTTCGTGCCGGGCCCCGTGAACATCCCGGACCCCGTGATCCG----------------
   |  |||     || || |  ||| |||  ||||        |||            | |   |  |    |    ||  |   ||   ||    |       | |            ||||||||||||||||||||| || ||||||| ||||||||||||||| || || ||||||||||||||||  ||||||||                
tttcagaaggttatattaggcaggagtttttattgct-------gtgggacgaataattattttttgtttgggcctgatgggcctttgtgtgtgtgtgtgtgggcagG----------GAGATGGCGGACTACGTGTATGGGCCGGGGCGGAACCACCTGTTCGTGCCTGGGCCGGTGAACATCCCGGACCAGGTGATCCGCGCCATGAGCCGTCAG

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|76918900|gb|DV167499.1|DV167499

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGCAG                       
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-CA-CAGgtacgcctgt ... gtaccagc

EST: gi|50327008|gb|CO522134.1|CO522134

EST:     GCTAG-TACCAGCAG                         CAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGG
genomic: GCTAGCTACCA-CAGgtacgcctgt ... gtaccagcagCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGG

EST: gi|78109038|gb|DV527455.1|DV527455

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAGCAG                 
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAG------C--TACCA-CAGgtacgcctgt ... gt

EST: gi|71437747|gb|DR818797.1|DR818797

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAGCAG                 
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAG------C--TACCA-CAGgtacgcctgt ... gt

EST: gi|211445898|gb|FL403745.1|FL403745

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAG                         CAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGA
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgt ... gtaccagcagCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGA

EST: gi|93014857|gb|EB640377.1|EB640377

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAGCAG                 
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAG------C--TACCA-CAGgtacgcctgt ... gt

EST: gi|148938194|gb|EC882479.2|EC882479

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAGCAG                 
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAG------C--TACCA-CAGgtacgcctgt ... gt

EST: gi|211232280|gb|FL414442.1|FL414442

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCATCTAGCTACCACAG                         CAAGAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGA
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgt ... gtaccagcagCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGA

EST: gi|148959061|gb|EE010556.2|EE010556

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAGCAG                 
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAG------C--TACCA-CAGgtacgcctgt ... gt

EST: gi|148957248|gb|EC903268.2|EC903268

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAGCAG                 
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAG------C--TACCA-CAGgtacgcctgt ... gt

EST: gi|149075108|gb|EE163598.2|EE163598

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAGCAG                 
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAG------C--TACCA-CAGgtacgcctgt ... gt

EST: gi|33467631|gb|CF244680.1|CF244680

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAGCAG                 
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAG------C--TACCA-CAGgtacgcctgt ... gt

EST: gi|211376270|gb|FL028048.1|FL028048

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAGCAG                 
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAG------C--TACCA-CAGgtacgcctgt ... gt

EST: gi|149008924|gb|EE041144.2|EE041144

EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGCAG                       
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-CA-CAGgtacgcctgt ... gtaccagc

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 2 RNA-Seq libraries.

Block sizes: 36 (upstream exon), 47 (downstream exon)
Score: 17

TTTGATGTTTCACAAACGCGTGAGCGGCTCGCCCTCCTCTCCAGTCCCTCCTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgt ... gtaccagcagCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGACCCACCTGTTCGTGCCGGGCCCCGTGAACATCCCGGACCCCGTGATCCG

Block sizes: 19 (upstream exon), 47 (downstream exon)
Score: 2

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcactacgctgacactccctcctctccctgcgtgcactgctgctagtaccagcagCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGACCCACCTGTTCGTGCCGGGCCCCGTGAACATCCCGGACCCCGTGATCCG

      cgctgac  putative branch site (score: 2)

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcgtaagtaaggatcagtctagaggtttggttgccaagttcagtgcactacgctgacactccctcctctccctgcgtgcactgctgctagtaccagcagCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGACCCACCTGTTCGTGCCGGGCCCCGTGAACATCCCGGACCCCGTGATCCG

- - - - - - - - - - - - - - tggttgc
- - - - - - - - - - - - - - - - - - - - - - -gcactac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgctg