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

...ttggtccaaagctacaaattcattgttgattcatcataacacttcatatatttgctggttattctaatctgatgatttttctgctgtgtgcgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGGAACCAACACCTCGGAAGAGCCAGAACGTCCGTTTGGACAGAGTGAGGAC

Basic information

species	Zea mays
transcript	GRMZM2G052855_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g36110.2 (Oryza sativa), 3'ss of exon 6

---------------ttggtccaaagctacaaattcattgttga----ttcatcataac-acttca------tatatttgctggttattctaatctgatgatttttctgctg--tgtgcgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGGAACCAACACCTCGGAAGAGCCAGAACGTCCGTTTGGACAGAGTGAGGAC
                   |   ||| |||   ||   || |      ||  || || | | ||||      |||  | |    ||  ||| ||      | | || ||||   ||| | |  ||||||||| |||||||| ||||||||||| ||||||||||||||     |||  | || |||||| |  ||| | |||| |  ||||||  ||||| ||| || 
gttggttccttttccaaattttgaagttaccgtttgtgtgctaggtcttttctcctatccaattcagtgttttatcctagtacatttctcttattcatctaatcttatgctctttgtactttttacagAAATCATTGTTTCTGGAGGAATGACCATGCCGCAGGTGATTGCAGCACCAGGACAAACACCCCATAAGGGTCAGAGCACCCGTTTAAACAGAATGATGAG

upper sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 6

ttggtccaaagctacaaattcattgttgattcatcataacacttcatatatt--tgctggttattctaatctgatgatttttctgctgtgtgcg--tgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGGAACCAACACCTCGGAAGAGCCAGAACGTCCGTTTGGACAGAGTGAGGAC
    |   ||  |     ||     |       |   ||  ||| | |||||  |     || ||||||| | ||| | |   ||   | ||    || | ||||||| |||||||| ||||||||||||||||| ||| ||||     || |||||       ||||   ||   | |  |||  |||| ||||| |  |   
----ttagaactttgtcgtttggcttctgcatgttgaaattcttaaaatattattttcatttcttctaattttatggtgtacatgtcttttgatgctgatgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTGGATA

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|89249399|gb|DY621185.1|DY621185

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTTTATTGGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAAGGATTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|88752753|gb|DY536894.1|DY536894

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|110525608|gb|EE029792.1|EE029792

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|60397295|gb|DN230111.1|DN230111

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|32935666|gb|CF040478.1|CF040478

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGTAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|76929387|gb|DV171992.1|DV171992

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|148995086|gb|EE034390.2|EE034390

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTTTATTTGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|113853357|gb|DW973994.1|DW973994

EST:     CTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGGCCGCAGGTGATCATGTCACTG
genomic: CTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATG-CCGCAGGTGATCATGTCACTG

EST: gi|71319563|gb|DR796526.1|DR796526

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|148985826|gb|EE029793.2|EE029793

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCANGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|14245263|gb|BG873845.1|BG873845

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|71774958|gb|DR972836.1|DR972836

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|78109866|gb|DV528282.1|DV528282

EST:     AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAG                         AAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG
genomic: AAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

EST: gi|78109865|gb|DV528281.1|DV528281

EST:     TGAAGGCATAG                         AAAT-ATTGTTTCAGGAGGAATGATTATGCCGCAGGTGATCATGTCACTGG
genomic: TGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGG

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: 46 (upstream exon), 48 (downstream exon)
Score: 73

AGTGTTTATGTGCCAACCAATCATTTATATATTGGTGACATCTTTTTGGTAAACTCCGCCGAAATTATAAGGCCCAATTTGTCTATTCGTGAAGGCATAGgttggttcct ... cgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGGAACCAACACCTCGGAAGAGCCAGAACGTCCGTTTGGACAGAGTGAGGAC

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 44

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 36

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 107

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atatatttgctggttattctaatctgatgatttttctgctgtgtgcgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGGAACCAACACCTCGGAAGAGCCAGAACGTCCGTTTGGACAGAGTGAGGAC

             ttattctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtccaaagctacaaattcattgttgattcatcataacacttcatatatttgctggttattctaatctgatgatttttctgctgtgtgcgtgctacagAAATAATTGTTTCAGGAGGAATGACTATGCCGCAGGTGATCATGTCACTGGAACCAACACCTCGGAAGAGCCAGAACGTCCGTTTGGACAGAGTGAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - -ctacaaa
- - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - -cacttca
- - - - - - - - - - - - - - - - - - - - - - - - - tttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatga