ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactctttacttgcaagcctttcacatgtatctttaattcttcactccatcttcacagacaatccttttctatgtag

Basic information

species	Zea mays
transcript	GRMZM2G402242_T03
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G402242_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 5'ss of exon 4

TGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactctttacttgcaagcctttcacatgtatctttaattcttcactccatcttcacagacaatccttttctatgtag
  |||| ||||| ||  | |||||||||||||||||||||||||| ||||||||||| |||||||| |||||||| || ||||| |||||||||||||||||| |  ||||||||     |    ||  | | |   | |  |   |  | ||| || | |||||||||| | |    
AATTTCTTATAAGGACCTCTATGGCTGGACAATGGATGATATTGTGAAAGCAATTGGCCTAAAAAATAATTGTACCTTTTGTGGTGTTTTTCGACGTCAGgtaattcttacttgcctctttggtgcaattttttactagttataggttaagctttactgccaatccttttttctag--

upper sequence: GRMZM2G402242_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 5'ss of exon 5

TGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactctttacttgcaagcctttcacatgtatctttaattcttcac---tccatcttcacagacaatccttttctat-gtag
 ||||||||||| ||  | |||||||||||||||||||||||||| ||||||||||| |||||||| || ||||| || ||||| |||||||||||||||||| |  || |||||    ||||      | | ||  | |  | |    |  | ||| || | |||||||||| | | ||||
AGTTTCCTATAAGGACCTCTATGGCTGGACAATGGATGATATTGTGAAAGCAATTGGCCTAAAAAATAACTGTACCTTTTGTGGTGTTTTTCGACGTCAGgtaattcttccttgcc--tctttggtgcattttttgtactacttataggttaagctttactgccaatcctttttttttgtag

upper sequence: GRMZM2G402242_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT2G44270.1 (Arabidopsis thaliana), 5'ss of exon 4

TGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactctttacttgcaagcctttcacat-gt---atctttaattcttcactccatcttcaca--gacaatccttttctatgtag-----------
|||||| ||||||||| ||||||| |||||||||||||| ||||| |||   |||||| | || |||||||| || || ||||| || || || || ||||||      | |  |      ||    | ||   |  || | ||  ||| |   ||| || |    |||  || || | | ||            
TGTTTCATATAAAGATCTGTATGGATGGACAATGGATGAGATTGTGAAAATGATTGGTTTGAAGAACAATTGCACCTTTTGTGGTGTATTCCGTCGACAGgtagggagcagtgccgttttctttttgttgttcaactttcagtttgtcaataactctgcataccaccaacactcttgtgtttaattcatctcaag

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|74232164|gb|DT640078.1|DT640078

EST:     AATTGGTCTAAAAAACAATTTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: AATTGGTCTAAAAAACAATT-GTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|71774415|gb|DR972293.1|DR972293

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|71761950|gb|DR959887.1|DR959887

EST:     CAATGGGTTTAAAAAACAATTGTACTTTTTGTGGAGTTTTTTGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|37416521|gb|CF645910.1|CF645910

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGA
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGA

EST: gi|67014256|gb|CO443005.1|CO443005

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGCCGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|50323940|gb|CO519066.1|CO519066

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|91872706|gb|EB402663.1|EB402663

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTGTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|26558362|gb|CA830597.1|CA830597

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|87157289|gb|DY402078.1|DY402078

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|71770543|gb|DR968480.1|DR968480

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|91872707|gb|EB402664.1|EB402664

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|22472216|gb|BU036696.1|BU036696

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

EST: gi|50337086|gb|CO532212.1|CO532212

EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG

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: 41 (upstream exon), 47 (downstream exon)
Score: 46

TGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTG

Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 33

Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 38

Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 32

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactctttacttgcaagcctttcacatgtatctttaattcttcactccatcttcacagacaatccttttctatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG