ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtctttgcgatcccattggtctaaacagtttcctatgaagtctgcattactctgctgaacttttctctcgttatgataatttgagcaaatataattgccttctaactgctgtccattgctag

Basic information

species	Zea mays
transcript	GRMZM2G076885_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g55280.1 (Oryza sativa), 5'ss of exon 4

TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtctttgcgatcccattggtctaaacagtttcctatgaagtc--tgcattactctgctgaacttttctctcgttatgataatttgagcaaatataa-ttgccttctaactg-----ctgtccattgctag
||||||||||||||||| ||||| ||||||||| || |||| |||||||| || |||||||| ||||| ||||||||||||||||| ||||| |||||       || ||          | |||  | |  ||| ||||||  ||||||||||| |       || |||| |||    | ||| || ||| |||| || | | ||||||       | || ||| ||||
TATGCTTTTAATATATTTTCACATAATGCACCAATTGTTGAAAATGGGTACAATGAGGAGGAGATGAAGATGGTGAAGGAGACCAGAAAAATCTGGgta------tgtga-------aagccaaattgatgtctaggaagtcattgcattactctccatccaacttttctcttta----actttaagaaaacataaattacatcctaactttatgcttctctattcctag

upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G34420.1 (Glycine max), 5'ss of exon 4

TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtct-ttgcgatcccattggtctaaacagtttcctatgaagtctgcattactctgctgaacttttctctcgttatgataatttgagcaaatataattgccttctaactgctgtccattgctag
|||||||||||| |||||||||| |||||  | ||||||   || || | ||| || || |||||||||||||| ||||||||||||||||| |||||  ||    ||  ||   ||   | ||||  ||||  || |   | ||  | |   |   ||| |  |  ||  || |  |   |||  |  ||| |                             
TATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTTAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGGgtgggtaaactgaaattgaatctttataaattgtttattaggttttttgtttcatgttatggaa-tagttgctaattttact--cttgcacttatacag----------------------------

upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G05250.1 (Glycine max), 5'ss of exon 4

TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtct-ttgcgatcccattggtctaaacagtttcctatgaagtct-gcattactctgctgaacttttctctcgttatgataatttgagcaaatataattgccttctaactgctgtccattgctag
|||||||||||| ||||||| || |||||  | ||||||   ||||| ||||| || || |||||||||||||| ||||||||||||||||| |||||  ||    ||  ||   ||   | ||||  ||||  || |   | | |  | |   |   |||   ||     ||| |      |||  |   || |                             
TATGCTTTTAATCTATTCTCGCATAATGCGTCTGTTCTTTCAAATGGATATAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGGgtgggtaagctgaaattgaatctttataaattgtttattaggtttttttgtttcatgttatggaatagttgctaagttttacc--cttgcacttctacag----------------------------

upper sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0011g05860.t01 (Vitis vinifera), 5'ss of exon 4

TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtctttgcgatcccattggtc-taaacagtttcctatgaagtctgcattactctgctgaacttttctctcgttatgata-atttgagcaaa-----------tataattgccttctaactgctgtccattgctag-------
|||||||||||| | || |||||||||||||| ||||||   |||||||| || || |||||||||||| | || || ||||| |||||||| ||||| ||| | ||   |   |||  |         | |    | || |    | | || || |    |||  |      ||| |  ||  |||| |            | || ||    |   |   || |   || |||        
TATGCTTTTAATCTCTTTTCACACAATGCACCTGTTCTTCCAAATGGGTACAATGAAGAGGAAATGAAATTAGTAAAAGAGACAAGGAAAATCTGGgtgagtttatgatcttttattccttgctcttcatatttggttaactagatacttctttgatagggtttgtttcgcagatgctggataggagccaggtcttaatttgtgtagtttatataacatgactttttgtttctatgttgtag

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|18964615|gb|BM661107.1|BM661107

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTA-CTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|7216942|gb|AW563049.1|AW563049

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|76292292|gb|DV031860.1|DV031860

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|5714254|gb|AI944239.1|AI944239

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|86470660|gb|DY237030.1|DY237030

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAAGTAACTGCGACTTGCATACGGGTTCCTGTGAT
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTG-AAAGTAACTGCGACTTGCATACGGGTTCCTGTGAT

EST: gi|7216973|gb|AW563095.1|AW563095

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|7227765|gb|AW566406.1|AW566406

EST:     GGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|78081782|gb|DV510194.1|DV510194

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|32934711|gb|CF039523.1|CF039523

EST:     GAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|93011814|gb|EB637334.1|EB637334

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|88749457|gb|DY533598.1|DY533598

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

EST: gi|78083842|gb|DV512235.1|DV512235

EST:     GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG                         AATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG
genomic: GGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATG

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), 47 (downstream exon)
Score: 161

TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtcttt ... ccattgctagAATGACAAGGAGGTGAAAGTAACTGCGACTTGCATACGGGTTCCTGTGATGCGCGCACATGCTGAAAGTGTCAATCTACAGTTTGAAAAGCCACTTGATG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 204

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

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

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGGgttagtctttgcgatcccattggtctaaacagtttcctatgaagtctgcattactctgctgaacttttctctcgttatgataatttgagcaaatataattgccttctaactgctgtccattgctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA