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

gtaaatccaaattctttttgatttatctcctcttcaaattggatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT

Basic information

species	Zea mays
transcript	GRMZM2G093557_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G093557_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g40850.2 (Oryza sativa), 3'ss of exon 3

gtaaatccaaattct-----ttttgatttatctcctcttcaaattg-------gatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT
|||| ||| || |||     ||||| | | | |  | ||    |||       | ||||| || ||| |   |  |  ||  | |||  ||  |  |||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| || || || || ||||||||||| ||||||||||||||||||||||| || 
gtaagtccgaagtctctcatttttgttatttataatgttttgcttgtttttttgttttgcattatgatgtctaatacttcacaaatttgttggctggattgaagATTGTTTGAGGAGGGTGGTGATTGGGAGAGGAAGAACAGATTGAAAGTGTACGAGGGCTTATACTGCATGGCCACTAGAAACTTCAAGAAAGCTGCAAGC

upper sequence: GRMZM2G093557_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G02940.1 (Glycine max), 3'ss of exon 4

--------gtaaatccaaattctttttgatttatctcctcttcaaattggatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT
         | |||   ||   | |||  ||   |       || |||   |||  ||| |  ||  | |    || |||  |     || ||     ||||||||||| |||||||||||||||||||||||||| ||  ||||||| || |||||  ||||||||||| | ||| |||| ||| |||| ||||| |  
gtaatgctttgaattacaaacatctttagttatgccttctgccatatt---tttctgtt-tagagtcggttt--tctaactgttcacatcatggcgacagCTTGTTTGAAGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTACGAAGGACTGTACTGCATGTCCACTCGAAATTTCGAGAAGGCTGCCAAG

upper sequence: GRMZM2G093557_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G02980.1 (Glycine max), 3'ss of exon 4

--------gtaaatccaaattctttttgatttatctcctcttcaaattggatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT
         | |||   ||   | | |  ||   | |     || |||   |||  |||  | || || |    || |||  |     || ||   | ||||||||||| |||||||||||||||||||||||||| ||  ||||||| || |||||  ||||||||||| | ||| |||| |||||||| ||||| |  
gtaaggctttgaattacaaacatctgtagttatgccctctgccatatt---tttctgtta-ggagttggttt--tctaactgttcacatcatggcggcagCTTGTTTGAAGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTACGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG

upper sequence: GRMZM2G093557_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G13640.1 (Glycine max), 3'ss of exon 4

--------gtaaatccaaattctttttgatttatctcctcttcaaattggatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT
         | |||   ||   | | |  ||   | |     || |||   |||  |||  | |   | |    || |||  | |   ||  | | | |||||||||||||||||||||||||||||||||||||| ||  ||||||| ||||||||  ||||||||||| | ||| |||| |||||||| ||||| |  
gtaatgctttgaattacaaacatctgtagttatgccctctgccatatt---tttctgttaagtattggttt---tctaactgtttacatcacggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTATGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG

upper sequence: GRMZM2G093557_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G24820.2 (Arabidopsis thaliana), 3'ss of exon 4

gtaaat-ccaaattctttttgatttatctcctcttcaaattggatt-tgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT
||||||  ||| ||   | |  |||  || |||||||   |||||  |||    ||||     | || |   || ||   | | |   |   || |||||||| || |||||||| ||||| ||||||||| |  | || || |||||||| |||||||||||| | || ||||| || ||||| ||||| || 
gtaaatgtcaatttggctgtattttgactactcttca---tggatagtgcaac-tgaaatccttgaattaacactttccgttttcccttgccagATTGTTTGAAGAGGGTGGTGACTGGGAGAGGAAGAACCGGCTAAAGGTCTATGAAGGTTTGTACTGCATGTCCACCAGAAATTTTAAGAAGGCTGCCAGC

upper sequence: GRMZM2G093557_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g10250.t01 (Vitis vinifera), 3'ss of exon 4

----------gtaaatccaaattctttttgatttatctcctcttcaaattggatttgcgttgtgaagctgataaagtccaacattgtttctcc-tgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT
           | |||  | ||| || ||  ||| |   |     |||    | |  |    |  |  || |    | | | |||||||   | ||  || ||||||||||| || || ||||||||||||||||||||| | ||||| || ||||||||  ||||||||||| | ||||||||||||||||| || || | |
cttttcttcttttaat--atatttttcttcgtttctgatcaaaaaaaaaaaaaataccacctttgatttgcttgttttcta-attgtttaaacatggatgcagCTTGTTTGAAGAGGGAGGTGATTGGGAAAGGAAGAACCGTTTGAAGGTGTATGAAGGCCTGTACTGCATGTCCACTAGAAACTTCAAGAAGGCAGCCAAT

upper sequence: GRMZM2G093557_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ25080 (Selaginella moellendorffii), 3'ss of exon 4

gtaaatccaaattctttttgatttatctcctcttcaaattggatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT
                                      | |||| |   ||||||   |             | ||       |||    |||||||| ||||| || ||||| ||||||||||||||| |  ||||||| || || ||| | ||||||||||| ||  | |||||||||||||||||    
-------------------------------------gtgggatgt---ttgtgattttttgtttacttggaactgacatgtttgacctcagCTTGTTCGAGGAGGGCGGTGACTGGGAAAGGAAGAACCGCCTGAAAGTTTACGAGGGGCTCTACTGCATGGCGACCCGGAACTTCAAGAAAGCTGCGGAG

upper sequence: GRMZM2G093557_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ29963 (Selaginella moellendorffii), 3'ss of exon 4

gtaaatccaaattctttttgatttatctcctcttcaaattggatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT
                                      | |||| |   ||||||   |             | ||       |||    |||||||| ||||| || ||||| |||||||| |||||| |  ||||||| || || ||| | ||||||||||| ||  | |||||||||||||||||    
-------------------------------------gtgggatgt---ttgtgattttttgtttacttggaactgacatgtttgacctcagCTTGTTCGAGGAGGGCGGTGACTGGGAAAGAAAGAACCGCCTGAAAGTTTACGAGGGGCTCTACTGCATGGCGACCCGGAACTTCAAGAAAGCTGCGGAG

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|211404635|gb|FL001886.1|FL001886

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|32847352|gb|CD987033.1|CD987033

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|26557213|gb|CA829448.1|CA829448

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|60341089|gb|DN208062.1|DN208062

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|78091767|gb|DV520141.1|DV520141

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|148966222|gb|EE017178.2|EE017178

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|32910411|gb|CF015223.1|CF015223

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|29167774|gb|CB411034.1|CB411034

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAG
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAG

EST: gi|149045875|gb|EE047873.2|EE047873

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|29167760|gb|CB411020.1|CB411020

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|149112312|gb|EE295203.2|EE295203

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|71444762|gb|DR825812.1|DR825812

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

EST: gi|148973310|gb|EE024395.2|EE024395

EST:     TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA
genomic: TTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATA

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), 47 (downstream exon)
Score: 164

CTGTTGGGCAAAAGATGGACCTTGTTTTCTACACACTACAAATTGGATTGTTCTATATGGACTTTGATCTCATCTCGAAGTCCATTGACAAAGCGAAAAAgtaaatccaa ... ctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 97

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 73

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 137

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attggatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT

                                           tcctgat  putative branch site (score: 137)
                                    ttgtttctcct  CT-rich tract
                     tgataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatccaaattctttttgatttatctcctcttcaaattggatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT