ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattctttatctatatttcttggagataaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa...

Basic information

species	Zea mays
transcript	GRMZM2G112865_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g62210.1 (Oryza sativa), 5'ss of exon 5

AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattctttatctatatttcttggagataaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttg-gcattgttacatccaaa-----
  | |||||||| || ||||| ||| | ||  |||| |||||||| |||||||||||||| || ||||||||||| ||||||  |||| |   |||  || ||  |    ||| ||    |||   |  |     |||| |  | || |  | |||| ||  ||   |    |  ||       
GAACCGAGCTGGTGGGTACACCAGACTATTGCGAACTAGGATACGAGTTGGTGATGCTGCACCGATGGCATACATTGAgtaagcttctct---tatgatttttaaaatggaaaattg--atcagtgacctttccattgg-gttattagtcagttttttttttgcggggaattagtcagttttgt

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g38580.2 (Oryza sativa), 5'ss of exon 5

AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaa---cattctttatctat-atttcttggaga---taaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa
|||||||||||| || || |||||| |  |  | || |||||||| ||||| |||||||| |||||||||||||| |||||      ||| || | ||  ||  || ||| |    |||||||||  |   || | | |    ||   |  | || ||   |    ||      ||         
AGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGAgtatgtcttttccttgtttaccataactaggaaaattcaaaatttacatttgaatttctcattgctgtttgttgcaagtgttctggtctgatgcaattcg-------

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g38580.1 (Oryza sativa), 5'ss of exon 5

AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaa---cattctttatctat-atttcttggaga---taaaatttaccgtcatatatttaa----aacttggagggagtaattggcttttcttggcattgttacatccaaa-------------------------------------------------------------------------
|||||||||||| || || |||||| |  |  | || |||||||| ||||| |||||||| |||||||||||||| |||||      ||| || | ||  ||  || ||| |    |||||||||  |   || | | |       |||  |  |||  |  | | |  |     | |||   | || |                                                                         
AGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGAgtatgtcttttccttgtttaccataactaggaaaattcaaaatttacatttgaatttctcattgctgtttgttgcaagtgttctggtctgatgcaattcgttttcttcatattcatttcaaagttgtaactattggactaacagacaagtacccttcatgttctattctattcatccgtttcag

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT5G64650.1 (Arabidopsis thaliana), 5'ss of exon 5

AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaaca----ttctttatctatatttcttggagataaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa
|||| ||||||| || |||||||||||| |  | ||  | || ||||||||||||||||| |||||||| || ||||||||| |    ||  || ||| ||||  ||  |    ||   ||  |   |  | || |   || |    ||| |          | |    || || ||   | 
AGATAGAGCTGGTGGATACACAAGAATGCTTCGTACTCGCATTCGTGTTGGTGATGCTGCCCCAATGGCCTATATCGAgtaaaacaagtttcttttctttattctttttaacagaagcatattgaattcgagtttag-tttagtcacagttac--aacaaaatggatgatgctatatttta-

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT5G09770.1 (Arabidopsis thaliana), 5'ss of exon 5

AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattctttatctatatttcttggagata--aaatttaccgtcatatat-----ttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa----------------------------
|||| ||||||| || ||||||||| || || | ||  | ||||| ||||||||||||||||| ||||| || ||||||||| | |  ||   | | ||| |  |   |      |||||  |||||| |     ||| | |    | | |||  |     |||    || || |      | ||                            
AGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGAgtaaaactagtttcttttctttatcagtctttctggttttacattcatatctccatgttagatcaaataagaagtgttaatgatttggaagctttctggtgaactaatttggtcgatacttgatactttggatag

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|32909297|gb|CF014109.1|CF014109

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|50337604|gb|CO532730.1|CO532730

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|110963515|gb|EE183415.1|EE183415

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|33099991|gb|CF059951.1|CF059951

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|37393499|gb|CF634015.1|CF634015

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGACAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|211500584|gb|FL212575.1|FL212575

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGA
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGA

EST: gi|211239658|gb|FL451920.1|FL451920

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|60353121|gb|DN220094.1|DN220094

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|60356193|gb|DN223166.1|DN223166

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|22490485|gb|BU050408.1|BU050408

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAAC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAAC

EST: gi|21987795|gb|BQ779323.1|BQ779323

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|32929716|gb|CF034528.1|CF034528

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|60397912|gb|DN230728.1|DN230728

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|87151864|gb|DY396653.1|DY396653

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCC

EST: gi|18965108|gb|BM661397.1|BM661397

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCC

EST: gi|50337603|gb|CO532729.1|CO532729

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

EST: gi|148963908|gb|EE015020.2|EE015020

EST:     TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA                         GTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC
genomic: TTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCC

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), 49 (downstream exon)
Score: 18

AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattct ... tcatatgcagGTTCGTGGATAGGGAGAATGAGCTTCGAGAGGCCAAACCTGCAACGCCGCCGCCTCCTCAACGAGTCCCTCTTGATCCATGGGCCAAGTCACGTGCTAGC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 4

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 7

Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 5

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGAgtaacattctttatctatatttcttggagataaaatttaccgtcatatatttaaaacttggagggagtaattggcttttcttggcattgttacatccaaa

- - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agataaaa