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

gtaactcaaataccctccgtttcgctcttttcttagtgcttacgtacctcgtaactggttgcctgcttcttgtgcctctctctctctctctctctccctcttcccgcgtggcgtgcgccgccgtacgggctgtttgctgctactgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT

Basic information

species	Zea mays
transcript	GRMZM2G095969_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 2

gtaactcaaataccctccgtttcgctcttttcttagtgcttacgtacctcgtaactggttgcctgcttcttgtgcctctctctctctctctctc-tccctcttcccgcgtggcgtgcgccgccgtacgggctgtttgctgctactgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT
                             | |  |   | | |   ||||   | |  |  |  | || |   | ||| || |||  ||||| |     ||| |  ||||   |  |   || |         |  | ||| |  |   ||||||||||||||||| ||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||| || |||||||| ||||||||
----------------------------gtacccacctcctcctctcctcacgattcttatctcgtttttctcggctcactgtctggctctcacgcttttctacttgcgtcttgctctttgctgc--------tgcgatgcgaacgaactgaagATGGCATGTTCAGGGGCATCTACCACGGCAAGCAATGCCACGCCGCCGACATCCCCGCCGTGCTCGCCCGCGCGTGGGCGGCCGGCGTCGACCGCATCAT

upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g06880.1 (Oryza sativa), 3'ss of exon 1

gtaactcaaataccctccgtttcgctcttttcttagtgcttacgtacctcgtaactggttgcctgcttcttgtgcctctctctctctctctctctccctcttcccgcgtggcgtgcgccgccgtacgggctgtttgctgctactgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT-
                            |  |    | ||      ||||   |||  |  |  | || | | |  || ||  ||  ||||| | |  ||| | |||||       | || | | |   ||   |||||| |  |   ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||| |||||  |||| ||||||||||| || |||||||| |||||||| 
---------------------------gtacccacctcctcctcctcctcccgactcttatctcgtttttcgcgtttcactgcctggctctcacgctttctactcgcgt----cttggcgtcttgct--cttgctgctgcgaacgaactgaagatggcatgttcagGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCCGCCGTGATCGCCCGCGCGTGGGCGGCCGGCGTCGACCGCATCATC

upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 1

gtaactcaaataccctccgtttcgctcttttcttagtgcttacgtacctcgtaactggttgcctgcttcttgtgcctctctctctctctctctctccctcttcccgcgtggcgtgcgccgccgtacgggctgtttgctgctactgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT
                                 ||   |   ||   |      | | ||     ||  || | |    ||| || |||  ||||| | |||  |   | ||||    | |  | | | |||   | ||| |  |   ||||||||||||||||| ||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| || ||| |||| || |||||||| ||||||||
--------------------------------gtataaccgccgcctcctcctcccgattcttatctcgtttttctcggctcactgtctggctctcacgcttttctacttgcgtcttgctctttgctg-ctgc--gatgcgaacgaactgaagATGGCATGTTCAGGGGCATCTACCACGGCAAGCAATGCCACGCCGCCGACATCCCCGCCGTGCTCGCCCGTGCGCGGGCGGCCGGCGTCGACCGCATCAT

upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G38780.1 (Glycine max), 3'ss of exon 2

gtaactcaaataccctccgtttcgctcttttcttagtgcttacgtacctcgtaactggttgcct-gcttcttgtgcctctctctctctctctctctccctcttcccgcgtggcgtgcgccgccgtacgggctgtttgctgctactgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT
                                           |  ||   |||       | | | ||    | | ||| | |||||||||||||| ||||                    | | ||     ||| |              |||||||||||| ||||| ||||||||||||||||| || |||| | | || ||  |  | ||  |     | || |||||||| ||||||   || || ||
-----------------------------------------gtgagccatttaatcaaacactttgttttccattcatctat-tctctctctctctctctct--------------------cattcgaaaaatttac--------------agATGGCATGTTTAAGGGAATCTACCACGGCAAGCAATGTCACGTCTCGGATATTGCAACTGTTTTGAACAGAGCTTGGGCTGCCGGCGTCACCCGAATTAT

upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0032g01170.t01 (Vitis vinifera), 3'ss of exon 2

gtaactcaaataccctccgtttcgctcttttcttagtgcttacgtacctcgtaactggttgcctgcttcttgtgcctctctctctctctctctctccctcttcccgcgtggcgtgcgccgccgtacgggctgtttgctgctactgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT
                                                         ||       |||||    | |    |  | |     || |    |   |  |          ||    |   |||     |   |    ||   ||||  |||||||||||| |||||| | ||||||||||||||||   | ||  |  | || ||  |     | || |||  ||| || || ||| | || ||
---------------------------------------------------------gtcaggcatttcttcgaacacatggtggcccatatgcttctctattttgttta--------tgcttctcaatctgcaaatt--caacctctgacagATAACATGTTCAAGGGAATCTACAATGGCAAGCAGTGCCACGTGTCTGATCTTGCAGCAGTGTTGAGCAGAGCTTGGAGTGCTGGTGTTGATAGAATTAT

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|71774366|gb|DR972244.1|DR972244

EST:     GACATCGCAGTCAACTTCACAG                         ATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA
genomic: GACATCGCAGTCAACTTCACAGgtaactcaaa ... tgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA

EST: gi|74242558|gb|DT650472.1|DT650472

EST:     GACATCGCAGTCAACTTCACAG                         ATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA
genomic: GACATCGCAGTCAACTTCACAGgtaactcaaa ... tgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA

EST: gi|94477631|gb|EB706589.1|EB706589

EST:     GACATCGCAGTCAACTTCACAG                         ATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA
genomic: GACATCGCAGTCAACTTCACAGgtaactcaaa ... tgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA

EST: gi|71325561|gb|DR799471.1|DR799471

EST:     GACATCGCAGTCAACTTCACAG                         ATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA
genomic: GACATCGCAGTCAACTTCACAGgtaactcaaa ... tgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA

EST: gi|76936926|gb|DV174965.1|DV174965

EST:     GACATCGCAGTCAACTTCACAG                         ATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA
genomic: GACATCGCAGTCAACTTCACAGgtaactcaaa ... tgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA

EST: gi|211484453|gb|FL145754.1|FL145754

EST:     GACATCGCAGTCAACTTCACAG                         ATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGTCGCCGACA
genomic: GACATCGCAGTCAACTTCACAGgtaactcaaa ... tgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA

EST: gi|76021692|gb|DT948862.1|DT948862

EST:     GACATCGCAGTCAACTTCACAG                         ATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA
genomic: GACATCGCAGTCAACTTCACAGgtaactcaaa ... tgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA

EST: gi|78108903|gb|DV527320.1|DV527320

EST:     GACATCGCAGTCAACTTCACAG                         ATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA
genomic: GACATCGCAGTCAACTTCACAGgtaactcaaa ... tgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACA

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: 48 (upstream exon), 49 (downstream exon)
Score: 67

CCCGGACTGACCCTCTGCCTTCACCTTGCCCTCCACCCCCCTCCCTCCCCTTCTGCGGCCGTGGCGAGCACCCCACCAGACATCGCAGTCAACTTCACAGgtaactcaaa ... tgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT

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

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 72

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 33

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcttcccgcgtggcgtgcgccgccgtacgggctgtttgctgctactgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT

                                            ctgcctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactcaaataccctccgtttcgctcttttcttagtgcttacgtacctcgtaactggttgcctgcttcttgtgcctctctctctctctctctctccctcttcccgcgtggcgtgcgccgccgtacgggctgtttgctgctactgccttgaagATGGCATGTTCAAGGGCATCTACCACGGCAAGCAGTGCCACGCCGCCGACATCCCGGCCGTACTCGCGCGCGCGTGGGCTGCAGGCGTCGATCGCATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG