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

...ccctttcctcatttccattatatctcataacctgaaaatgaatgaggtgcaggtgcttgtgggtgcattctgaaatgtaactattttcttctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA

Basic information

species	Zea mays
transcript	GRMZM2G008327_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 2

---ccctttcctcatttccattatatctcataacctgaaaatgaatgaggtgcaggtgcttgtgggtgcattctgaaatgtaactattttcttctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA
      | ||  |||| |  ||  || ||||  | |||  | ||| | |    || |  |||||| |||||  || ||||| ||| |||||||||||||||||||||| ||||| |||||||||| ||| ||||| ||||| |||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||| |
aaaatgtgtctacattcctgttgcat-tcatg-cttgacca-gaaagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttctccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4

---ccctttcctcatttccattatatctcataacctgaaaatgaatgaggtgcaggtgcttgtgggtgcattctgaaatgtaactattttcttctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA
      | ||   ||| |  ||  || ||||  | |||  | ||| | |    || |  |||||| |||||  || ||||| ||| |||||||||||| ||||||||| ||||| |||||||||| ||| ||||| ||||| |||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||| |
aatatgtgtctaaattcctgttgcat-tcatg-cttgacca-gaaagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3

ccctttcctcatttccattatatctcataacctgaaaatg---aatgaggtgcaggtgcttgtgggtgcattctgaaatgt--aactattttct---tctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA
        | ||||   | ||   | |||    | | |||   | |  |||| |  | |  ||  ||      | |||| |  || | |||  |    |||||| |||   | ||| || || || |||   ||  |||| ||||| ||||| ||||||||||||||||||||||||||||| || || || ||||||||||| || |
-------tttatttt-gtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattctttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 2

ccctttcctcatttccattatatctcataacctgaaaatgaatgaggtgcaggtgct-tgtgggtgcattctgaaatg-taactattttc------ttctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA
        ||      || ||   || | |  |||| |||  | |  |     ||   | |     ||   |||  |  | |  |||||       | |||||| |||   | ||| ||||| || |||   ||  |||| ||||| ||||| ||||||||||||||||||||||| ||||| || || || |||||||||||  |||
--------tccaccttatcatgcatcgttaattgaatatgttttattttttattgtggtttcaaaacaagatgagctaattaaaatttttaaatgatgctttctgcagATGTTCCTGTACCAAATTCTCTGTGGCATTGCATACTGTCATTCACATAGAGTTCTTCATCGAGACTTAAAACCACAGAATTTGTTGATAGATCGCAGCA

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 3

ccctttcctcatttccattatatctcataacctgaaaatgaatgaggtgcag-gtgcttgtgggtgcattctga---aatgtaactattttctt----ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA
        ||      |||||   || | |  |||| |    | |  |  |  ||| || |     ||   |||   ||| ||| | |||   |    |||||| |||   | ||| ||||| || |||   ||  | || ||||| ||||| | ||||||||||||||||||||| ||||| || || || |||||||||||  |||
-------ttccaccttattatggatcgttaattgaatacattttatttttatcgtggtt-tcaaaacaagatgagctaatttaaatttttaaatgatgctttctgcagATGTTCCTGTACCAAATTCTCTGTGGCATCGCTTACTGTCATTCACGTAGAGTTCTTCATCGAGACTTAAAACCACAGAATTTGTTGATAGATCGCAGCA

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 3

ccctttcctcatttccattatatctcataacctgaaaatg---aatgaggtgcaggtgcttgtgggtgcat-tctgaaatgtaactattttc----ttctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA
        ||  ||   | |    | |||    | | |||   | |  |||| |  | |  ||  ||     | | |||| | | |   ||     | |||||| |||   | ||| || || || |||   ||  |||| ||||| ||||| ||||||||||||||||||||||||||||| || || || ||||||||||| || |
--------tctattttgtcaagggttatataagggagatgctaattttggtgaaaataccagttagtttggatttaaaatttgaattccttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4

ccctttcctcatttccattatatctcataacctgaaaatgaatgaggtgcaggtgcttgtgggtgcattctgaaatgtaactattttcttct-----ttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA
    ||  | || || ||  | |    ||   | | | | | |   | |||  ||||||  | |  ||  ||  |||   ||  |  |   |      | | |||   | |||  | ||||| ||||  ||| |||| || || ||||||||||| |||||||||||||| ||||| || || |||||| | |||||||| || |
----tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagata-atggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA

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|78089349|gb|DV517723.1|DV517723

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|17921690|gb|BM259341.1|BM259341

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCATGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|60394106|gb|DN226976.1|DN226976

EST:     CCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA
genomic: CCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|87152029|gb|DY396818.1|DY396818

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCATGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|76017014|gb|DT944184.1|DT944184

EST:     GTTCATGGACTCCTGCCCGGAGTTTGGT-AGAAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCACGGGGTTGCGTACTGCCATTCTCATAGA
genomic: GTTCATGGACTCCTGCCCGGAGTTTGCTAAG-AATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|60394498|gb|DN227368.1|DN227368

EST:     TCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA
genomic: TCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|31362736|gb|CD447093.1|CD447093

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTGCATGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|7216555|gb|AW562677.1|AW562677

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCGTGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|6095562|gb|AW120229.1|AW120229

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         G
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccag-

EST: gi|6095562|gb|AW120229.1|AW120229

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         G
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccag-

EST: gi|22489528|gb|BU049451.1|BU049451

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCATGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|61118496|gb|DN559457.1|DN559457

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCATGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

EST: gi|93281356|gb|EB673620.1|EB673620

EST:     AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAG                         TCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA
genomic: AGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGA

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), 49 (downstream exon)
Score: 130

CGAGAAGCGCATATACCTTGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCCTGCCCGGAGTTTGCTAAGAATCCCACTTTGATCAAGgtgagaagcg ... ctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 84

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78

Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 49

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ggtgcaggtgcttgtgggtgcattctgaaatgtaactattttcttctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA

                             atgtaac  putative branch site (score: 49)
                                taactattttcttctt  CT-rich tract
                           aaatgtaactatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctttcctcatttccattatatctcataacctgaaaatgaatgaggtgcaggtgcttgtgggtgcattctgaaatgtaactattttcttctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA

- - - - - - - - - - - - - - -acctgaa
- - - - - - - - - - - - - - - - - - -atgaatg
- - - - - - - - - - - - - - - - - - - - - - -ggtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaaatg