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

...gtgtggccttgtccactgtatctggccatgtgttgaaaatgatattacacctagataatgcctttgctcgtatctgtaagtatttcatgtttcctggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAGAAGTTTTTGGCATACATGGCCCCAGCACCCCATGAG

Basic information

species	Zea mays
transcript	GRMZM5G806309_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G806309_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g06070.1 (Oryza sativa), 3'ss of exon 7

-----gtgtggccttgtccactgtatctggccatgtgttgaaaatgatattacacctagataatgcctttgctcgtatctgtaagtatttcatgtttcc-tggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAGAAGTTTTTGGCATACATGGCCCCAGCACCCCATGAG
      ||     | |  |  | ||| |    || ||       | ||| | ||||||| |||| || |||    |    |  |   ||| ||| |||| || |||||||||||||||||||||  ||||| |||||| |||||| ||||||| ||||| ||||| ||||||||||  ||| | |||||||||
gcaatatgcattttagatccatatatttttggatatgcc-----taatactccacctag-taatacccttgagtatcatcgagacattttgatgcttccatgacagGCTGTGATGAAAAGTTTTCTTGTCAATGGTTCGGACCCTGCAAAACAAGAGAAATTTTTAGCATACATGGTTCCATCCCCCCATGAG

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|5928962|gb|AW056254.1|AW056254

EST:     AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGG                         GCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAG
genomic: AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGGgtgagttctg ... ttcctggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAG

EST: gi|67015187|gb|CO443936.1|CO443936

EST:     AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGG                         GCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAAGAG
genomic: AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGGgtgagttctg ... ttcctggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAG

EST: gi|76286234|gb|DV025802.1|DV025802

EST:     AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGG                         GCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAG
genomic: AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGGgtgagttctg ... ttcctggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAG

EST: gi|76286235|gb|DV025803.1|DV025803

EST:     AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGG                         GCTGTGATGAA
genomic: AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGGgtgagttctg ... ttcctggcagGCTGTGATGAA

EST: gi|71765228|gb|DR963165.1|DR963165

EST:     AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGG                         GCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAG
genomic: AGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGGgtgagttctg ... ttcctggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAG

EST: gi|71765227|gb|DR963164.1|DR963164

EST:     CCTGTACGTGATGAATGTGAATCCCGG                         GCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAG
genomic: CCTGTACGTGATGAATGTGAATCCCGGgtgagttctg ... ttcctggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAG

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: 47 (upstream exon), 48 (downstream exon)
Score: 133

GGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGATTCTGAGCAGTACAACAAACTTGAGAGACCTGTACGTGATGAATGTGAATCCCGGgtgagttctg ... ttcctggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAGAAGTTTTTGGCATACATGGCCCCAGCACCCCATGAG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 119

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 107

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 107

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tacacctagataatgcctttgctcgtatctgtaagtatttcatgtttcctggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAGAAGTTTTTGGCATACATGGCCCCAGCACCCCATGAG

                                          tgtttcct  CT-rich tract
                               taagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtggccttgtccactgtatctggccatgtgttgaaaatgatattacacctagataatgcctttgctcgtatctgtaagtatttcatgtttcctggcagGCTGTGATGAAAAGTTTTAGTGTCAGTGGTTCAGACCCTTCAAAACAGGAGAAGTTTTTGGCATACATGGCCCCAGCACCCCATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - -ctgtatc
- - - - - - - - - - - - gccatgt
- - - - - - - - - - - - - - - - - gaaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgt