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

...aaataaaatatataatcttttgcctggaaaatatctctatttagctatgtttgaagcttgatttatctgaccttaaactgtatttgcccgtaccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCCGAGGAGTTAAAAAGAGACCCTGACAAGTGGATGATTGACATTGACTATT

Basic information

species	Zea mays
transcript	GRMZM2G149802_T02
intron #	23
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G149802_T02 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os01g64820.1 (Oryza sativa), 3'ss of exon 23

-aaataaaatatataatcttttgcctggaaaatatctctatttagctatgtttgaagcttgatttatctgaccttaaactgtatttgcccgtaccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCCGAGGAGTTAAAAAGAGACCCTGACAAGTGGATGATTGACATTGACTATT
  |||  | || | ||  | | |||     ||||  | | |  ||||||| ||||||| |  ||||||| ||||  | ||| || || || |   |  ||||| ||||| | | ||||||| |  ||||||||||| |||||||||||||| |||||| | |||||| |||||||||| ||||||||||| |||||||| |
ataattcactaaaaaaagtgtcgcc-aattaatacttatctcaagctatgcttgaagcatactttatctaacctagagctgcatctgaccattgtgagcagGATTCAGAGAGTACACATTCAGGAGGAATAGCTCAAAGAGCTAGACATCCAGAGGAGCTGAAAAGAAACCCTGACAAATGGATGATTGATATTGACTACT

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|32939296|gb|CF044115.1|CF044115

EST:     ACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: ACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC

EST: gi|211402399|gb|FL354720.1|FL354720

EST:     CTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: CTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC

EST: gi|32938785|gb|CF043604.1|CF043604

EST:     GTACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: GTACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC

EST: gi|32938920|gb|CF043739.1|CF043739

EST:     ACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: ACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC

EST: gi|74242013|gb|DT649927.1|DT649927

EST:     CTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: CTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC

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), 42 (downstream exon)
Score: 135

GTTGCTTTGAGACTCAAGCAAAATGGTTACTCTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCCGAGGAGTTAAAAAGAGACCCTGACAAGTGGATGATTGACATTGACTATT

Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 29

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 25

Block sizes: 48 (upstream exon), 31 (downstream exon)
Score: 22

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatgtttgaagcttgatttatctgaccttaaactgtatttgcccgtaccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCCGAGGAGTTAAAAAGAGACCCTGACAAGTGGATGATTGACATTGACTATT

                   atctgac  putative branch site (score: 22)
            ttgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaataaaatatataatcttttgcctggaaaatatctctatttagctatgtttgaagcttgatttatctgaccttaaactgtatttgcccgtaccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCCGAGGAGTTAAAAAGAGACCCTGACAAGTGGATGATTGACATTGACTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA