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

...gcgctatgtaaatcacatcggacaaacttttacttagatgctgaaaccttccagggatcgattgcttgatgttgtagttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA

Basic information

species	Zea mays
transcript	GRMZM2G083095_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 3'ss of exon 1

-------gcgctatgtaaatc-acatcggacaaacttttacttagatgctgaaaccttccagggatcgattgcttgatgttgtagttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA
       ||||||  |   ||      | | ||  | | ||  |||| |       |  |||       || ||| |     | | |      ||||  |||| ||||||||||| || ||||| || || ||  | |||||||| |||||||| ||||||||||| || ||||||||||||||||| || ||||||||||| |||||
tgctcctgcgctacatttttctgtgatgtataatatctgac--agattcatgttagtatcagaagctagtttcttaacagcatcgct------gttttgttttggtagGAATGAATAAGATGGTCATTAACCATCTCGACAAGCTCTTTGTCACGAACGATGCTGCAACAATTGTGAATGAGCTCGAGGTCCAGCACCCTGCTGCTAA

upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 1

gcgct-atgtaaatcacatcggacaaacttttacttagatgctgaaaccttccaggg-atcgattgcttgatgttgtagttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA
| |||  | | ||| |  | |   ||   |    ||   ||   | |  |   | |     | | |  |  | ||  | |  |  || |   ||  ||  ||||||||| || |||||||| ||||||||||||||||| |||||||| ||||||||||  || ||||||||||| || ||||||||||| ||||| || ||
gtgcttgtattaat-atgttgctgaagaatgcgtttgtttggatagatttagaatgttggtggtggtcttgttttcaaatgttttgtttgatctgatt-cagGAATGAATAAGATGGTTATAAATCACTTGGACAAGCTTTTTGTCACGAACGATGCTGGGACAATTGTGAATGAACTTGAAGTTCAGCATCCTGCTGCCAA

upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 1

gcgctat-gtaaatca--catcggacaaact-tttacttagatgctgaaaccttccagggatcgattgcttgatgttgtagttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA
| ||| |  | ||||       | | |||   |||  || |||      |   |   ||    | | |  |  | ||  | |  |  || |   ||  ||  ||| ||||| || |||||||| ||||||||||||||||| |||||||| ||||||||||  || ||||||||||| || ||||||||||| ||||| || ||
gtgcttttatgaatctgttgctgaagaaagggtttgtttggatagatttagaatgttgg---tggtggtcttgttttcaaatgttttgtttgatctgatt-cagGGATGAATAAGATGGTTATAAATCACTTGGACAAGCTTTTTGTCACGAACGATGCTGGGACGATTGTGAATGAACTTGAAGTTCAGCATCCTGCTGCCAA

upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 1

gcgctatgtaaatcacatcggacaaacttttacttagatgctgaaaccttccagggatc--gatt--gcttgatgttgtagttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA
    ||  | || ||     ||     |  |    || ||  |     ||| ||||||   ||||  | ||     || |||||| |   ||    | ||  ||||||||| ||||||||||||||||| |||||||| |||||||||||||| || ||||| || || ||||||||||||||  |||||||||| || |||||
---atagtttaagcaagcttgatctgttactgtaaaggtgaagtctttttctagggattcagattcggattagaactg-agttcttctgtttataatgtttcagGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATGACGCTGCTACTATAGTGAATGAGCTCGAGATTCAGCACCCGGCTGCTAA

upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 1
lower sequence: EDP06021 (Chlamydomonas reinhardtii), 3'ss of exon 1

----------gcgctatgtaaatcacatcggacaaacttttacttagatgctgaaacc---ttccagggatcgattgcttgatgttgta--gttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA
          |    |      |  ||||||     || |  |  | | |  |    |   ||   | |   ||  ||| |  | |  |  |    |  ||    |     ||||| |||||||| ||||| ||||| |||||||| ||||||||||| || | ||| ||   ||| || ||||  ||||| || || ||||| || || |||||
gtaatttgatgtcagactggtgtatcatcggtttggctctgcccgaaaagtcgggttcagattggcgcgcgtgacggctgggcgctaaaccggggccgctgcgcgcaacccgtagGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCGACGCGAGCACTATCGTGAGCGAGCTGGAGGTGCAGCATCCCGCGGCTAA

upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ21647 (Selaginella moellendorffii), 3'ss of exon 1

gcgctatgtaaatcacatcggacaaacttttacttagatgctgaaaccttccagggatcgattgcttgatgttgtagttctccgtgtt-tcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA
                                                 |    | |||||   |||  | |||   ||    |||   | | |     ||| |||||||| ||||| ||||||||| |||||||||||||||| || || || || |  |||||  |   |||||| ||||| ||||| || || || | 
------------------------------------------------gtgagtgaatcgagctctttgt-ttgcgcttgagtgtgagattcctggctcagGCATGAACAAGATGGTGATCAATCACCTGGACAAGCTGTTTGTGACGAATGACGCCGGGACCATCATCGGTGAGCTAGAAGTCCAGCATCCCGCGGCGAG

upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ33799 (Selaginella moellendorffii), 3'ss of exon 1

gcgctatgtaaatcacatcggacaaacttttacttagatgctgaaaccttccagggatcgattgcttgatgttgtagttctccgtgtt-tcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA
                                                 |    | |||||   |||  | ||||   |    |||   | | |     ||| |||||||| ||||| ||||||||| |||||||||||||||| || || || || |  |||||  |   |||||| ||||| ||||| || || || ||
------------------------------------------------gtgagtgaatcgagctctttgt-ttgtgcctgagtgtgagattcctggctcagGCATGAACAAGATGGTGATCAATCACCTGGACAAGCTGTTTGTGACGAATGACGCGGGGACCATCATCGGTGAGCTAGAAGTCCAGCATCCCGCGGCGAA

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|211339979|gb|FL217829.1|FL217829

EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG

EST: gi|211342372|gb|FL217845.1|FL217845

EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG

EST: gi|211342371|gb|FL217844.1|FL217844

EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG

EST: gi|211342368|gb|FL217841.1|FL217841

EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG

EST: gi|211339980|gb|FL217830.1|FL217830

EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG

EST: gi|211339977|gb|FL217827.1|FL217827

EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG

EST: gi|211339982|gb|FL217832.1|FL217832

EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG

EST: gi|148978584|gb|EE026233.2|EE026233

EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG

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: 218

GGCCACCGCCACCTCTCCGGGCTCGAGGAGGCCGTTCTCAAGAACATCGACGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 86

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

accttccagggatcgattgcttgatgttgtagttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA

                  gcttgat  putative branch site (score: 96)
                                ttctccgtgtttcctt  putative PPT
                                              tttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgctatgtaaatcacatcggacaaacttttacttagatgctgaaaccttccagggatcgattgcttgatgttgtagttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC