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

...gaccagttatcatcttgtttcatttcaccgagattggttttgtacgaatttgagctacatttggtatctgaccctgtgcaatgtacttgtttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA

Basic information

species	Zea mays
transcript	GRMZM2G040017_T02
intron #	10
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G040017_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g55940.2 (Oryza sativa), 3'ss of exon 9

-------gaccagttatca-tcttgtttcatttcaccgagattggttttgtacgaatttgagctacatttggtatctgaccctgtgcaatgtacttgtttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA
        | | | |||   |||  | | | ||  | |  || |||| ||     || | | | |      ||   ||| |    ||  | |   ||||||    ||||||||   ||||||||||||||||||||||||||||||| | ||||||||||||||||| ||||||||||| ||||| |||||||||||||| |
ttcacactatctgctatagctctcttatgaattacctggcataggttctg---atatctcaaccatcaccagt---tgatcacacgctctttctatgtttc--cacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA

upper sequence: GRMZM2G040017_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G00380.1 (Glycine max), 3'ss of exon 9

-gaccagttatcatcttgtttcatttcaccgagattggttttgt-acgaatttgagctacatttggtatctgaccctgtgcaatgtacttgtttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA
 ||   ||         ||||   |  |  |   ||  ||||||  | | | | |  ||  ||||  |    ||| | |  ||| |   |  ||| |||||||| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || ||||| || ||  ||    
tgatttgtgtgtgataggtttatatgtagagtatttttttttgttgccactattatttatgtttgtgac--aaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG

upper sequence: GRMZM2G040017_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 9

--gaccagttatcatcttgtttcatttcaccgagattggttttgtacgaatttgagctacatttggtatctgaccctgtgcaatgtacttgtttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA
  ||   ||         ||||   |  |  |   ||  |||  | | | | | |  ||  ||||  |    ||| | |  ||| | | |  |||  ||||||| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || ||||| || ||  ||    
ttgatttgtgtgtgataggtttatatatagagttttttttttgttgccactattacttatgtttgtgac--aaccattttaaatttgcgttattccatgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG

upper sequence: GRMZM2G040017_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 9

-gaccagttatcatcttgtttcatttcaccgagattggttttgt-acgaatttgagctacatttggtatctgaccctgtgcaatgtacttgtttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCC-ACAATCAA---
 ||   ||         ||||   |  |  |   ||  ||||||  | | | | |  ||  ||||  |    ||| | |  ||| |   |  ||| |||||||| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || ||||| || || | ||       
tgatttgtgtgtgataggtttatatgtagagtatttttttttgttgccactattatttatgtttgtgac--aaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGGTGA

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|211272295|gb|FL440029.1|FL440029

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACCGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|149085153|gb|EE174657.2|EE174657

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATTTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|211010290|gb|FL457993.1|FL457993

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|91868897|gb|EB400200.1|EB400200

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|32837305|gb|CD976983.1|CD976983

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGAT
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGAT

EST: gi|32836604|gb|CD976282.1|CD976282

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|148972711|gb|EE023671.2|EE023671

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

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), 49 (downstream exon)
Score: 139

TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 185

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gaatttgagctacatttggtatctgaccctgtgcaatgtacttgtttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA

                    atctgac  putative branch site (score: 185)
                                        cttgtttc  putative PPT
          tacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaccagttatcatcttgtttcatttcaccgagattggttttgtacgaatttgagctacatttggtatctgaccctgtgcaatgtacttgtttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC