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

gtaggatttctacaaaatttccccatttcatacacattattcaaacaatgtcttagtgatacttttatttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATTTATGGACACCAAGAAGGGATGCGATCAGACTACTAGACAGCTTCGAATG

Basic information

species	Zea mays
transcript	GRMZM2G143246_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 7

gtaggatttctacaaaatttcccc---atttcatac--acattattcaaaca--atgtcttagtgatacttttatttgt--acaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATTTATGGACACCAAGAAGGGATGCGATCAGACTACTAGACAGCTTCGAATG
|||||||       |  ||| | |   ||| || ||  | || |||||  ||  |||  ||  ||||    || ||||     |||| ||||||||||||||||||||||||||||||| ||||| || ||||||||||||||||| ||||||||||| ||||| |  |||||||||||||| |||
gtaggatccgcgtgaccttttctcttcattacacactgaaatgattcattcagaatgcattgatgatgaaattctttgatgttaagGTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATTTATGGACACGAAGAAGGGATGTGATCAAATCACTAGACAGCTTCGGATG

upper sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 7

gtaggatttctacaaaatttcc----ccatttcat---acacattatt-caaacaatgtcttagtgatacttttatttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATTTATGGACACCAAGAAGGGATGCGATCAGACTACTAGACAGCTTCGAATG
||||||| | | | |  ||| |     | || |||   |||| ||||  || |      | |  ||     ||  | | |   ||  |||| ||  | || || || || |||||||| ||||||||  | ||||||||||| ||||| || ||||| ||||||| |||||| || || || |||
gtaggatgtgttctaccttttcattctcgttgcatttaacaccttatcacatatggccacctgatggagtcttcctatttttcagATTGGTAAAGTTGCTAGAAGACATCATGGATGGCAGCCGAATACTGATATTTATGGATACCAAAAAAGGATGTGATCAGATTACTAGGCAACTCCGCATG

upper sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 7

---------------------------gtaggatttctacaaaatttccccatttcatacac-attattcaaacaatgtcttagtgatac-ttttatttg-tacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATTTATGGACACCAAGAAGGGATGCGATCAGACTACTAGACAGCTTCGAATG
                             ||  |||  ||   ||    | |  ||||     |||      |  |  ||||| | ||   ||| |  |  |   ||  |||| ||  | ||||||||||| ||||||||  |||||||| | ||||| |||||||| ||||| || || || |||| |||| | |||||||| |||
gtaaggccatattaaatgtgattgtttaaagattttaaactttatacttctacatcatgtgggattgggtgcaggac-tcttaataatttgtttcacataatttcagATTGGTGAAGTTGCTGGAGGATATTATGGATGGCGGCCGAATTCTTATATTCATGGACACTAAGAAAGGGTGTGACCAGATTACTCGGCAGCTTCGCATG

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|33092549|gb|CF052543.1|CF052543

EST:     GCCATTGTTCAGCATGTGGAGATATTATCTGAGAGTCAGAAGTATAACAA                         GCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT
genomic: GCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT

EST: gi|9255282|gb|BE345750.1|BE345750

EST:     TGAGAGTCAGAAGTATAACAA                         GCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT
genomic: TGAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT

EST: gi|60350175|gb|DN217148.1|DN217148

EST:     AGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAA                         GCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT
genomic: AGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT

EST: gi|32910886|gb|CF015698.1|CF015698

EST:     GAGAGTCAGAAGT-TAACAA                         GCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT
genomic: GAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT

EST: gi|71774215|gb|DR972093.1|DR972093

EST:     AGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAA                         GCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT
genomic: AGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT

EST: gi|60342571|gb|DN209544.1|DN209544

EST:     GCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAA                         GCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT
genomic: GCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT

EST: gi|31349821|gb|CD434178.1|CD434178

EST:     GCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAA                         GCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT
genomic: GCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT

EST: gi|76287086|gb|DV026654.1|DV026654

EST:     GCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAA                         GCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT
genomic: GCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT

EST: gi|211150648|gb|FL192881.1|FL192881

EST:     GCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAA                         GCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATT
genomic: GCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATT

EST: gi|9255412|gb|BE345880.1|BE345880

EST:     AGAGTCAGAAGTATAACAA                         GCTGG-TAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT
genomic: AGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATT

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), 48 (downstream exon)
Score: 200

GTCACTATTGGTTCTGAAGACTTGAAGGCTAATCATGCCATTGTTCAGCATGTAGAGATATTATCTGAGAGTCAGAAGTATAACAAgtaggatttc ... tttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATTTATGGACACCAAGAAGGGATGCGATCAGACTACTAGACAGCTTCGAATG

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

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ccatttcatacacattattcaaacaatgtcttagtgatacttttatttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATTTATGGACACCAAGAAGGGATGCGATCAGACTACTAGACAGCTTCGAATG

                                       cttttattt  CT-rich tract
                                    atacttttatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggatttctacaaaatttccccatttcatacacattattcaaacaatgtcttagtgatacttttatttgtacaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATTTATGGACACCAAGAAGGGATGCGATCAGACTACTAGACAGCTTCGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG