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

...tatcaagtatttgaagaccggagggagtacctcccttgtcctttttacacaaaaaactgatacattcttatggatgtatctctacttttgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT

Basic information

species	Zea mays
transcript	GRMZM2G351417_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G351417_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 2

-----------tatcaagtatttgaagaccggagggagtacctcccttgtcctttttacacaaaaaactgatacattc-ttatggatgtatctctacttttgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT
           |||   || ||||  |    | |   ||||      |     |  |   |  |   ||  |   |   |     |  ||| |  |    |   | |||||||| ||||||||||| |||||||||||||||||||||||||| || ||||| |||||||| ||||||||||||||||| |||||  ||||||||||||| |
gtatgcaactttattttgtttttggtggattgcgatggtactggtgatacatgtactgttcttattgctactgtttagatggctaacttattttaatggatatatcttgcagACCAGGAAAGATGCAACTCAAGTTGTTGCAAACTTGCAAAGGCAGCAAGTCTCCTCAAAAATAGTTGCATCTGAGTATCTAGAAGCAAATAAAGATCTTT

upper sequence: GRMZM2G351417_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 2

---------------------------------------------------------------------------------tatcaagtatttgaagaccggagggagtacc---tcccttgtccttttt-acacaaaaaactgatacattcttatg-gatgtatctctacttttgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT
                                                                                 ||| ||| | |   |  | ||  |  ||      || | |||   |||| |  |   |     ||   ||  |||  | |   |       | ||    |||||| | || |||||||| ||||||||||||||||| || ||||| ||||| ||    |  ||| |  |||||||||| ||||| |||  |||||  |||||  
gtagtaaagaaatttatgatagacctcctgatatttgcactgtttgatgctgttagataccctttgtaggattggtatgcttattaagaaataagaatctgggtgatgtgtggaatcacatgtttattttgatgctgtactgcaattgtttactatttggtaacttggagactatgggctttgcagGCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTA

upper sequence: GRMZM2G351417_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G12220.1 (Glycine max), 3'ss of exon 2

--tatcaagtatttgaa-gaccggagggagtacctcccttgtcctttttacacaaaaaactgatacattcttatggatgtatctctacttttgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT
   |  ||| || ||   || | | || |  || |   || |  |  |     |      |  |  | | || |||     |    ||| | |  | |||||| | || |||||||| ||||||||||||||||| || ||||| ||||| ||    |  ||| |  |||||||||| ||||| |||  |||||  |||||  
agaaataagaatctgggtgatcagtggaatcacatgt-ttattttgatgctgtactgcgattgtttactatt-tggtaacctggagactatgggct-ttgcagGCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTA

upper sequence: GRMZM2G351417_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 2

tatcaagtatttgaagaccggagggagtacctcccttgtcctttttacacaaaaaactgatacattcttatggatgtatctctacttttgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT
  | |  | | |    |  |||  ||       | |  |  ||   | |||    |    |  |||   |   || | ||  |  |||| | |     |||| |||||||||||||| ||||||||||||||  | || || ||||| ||    |||  | |  |||| ||||| ||  ||||  | || |  |||||| 
-gtaacatttctccgtataggaaaga-------catcatttttgagatacattggatgattgaattgcgaaaaatctgtcctttttttttaat----tagACGAGGAAAGATGCTACACAAGTTGTTGCAAATCTACAGAGGCAACAGGTTAATTCACGGTTGATTGCTTCTGATTATTTAGAAGCCAACATTGATCTCA

upper sequence: GRMZM2G351417_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G17270.1 (Arabidopsis thaliana), 3'ss of exon 2

-tatcaagtatt-tgaagaccggagggagtacctcccttgtcctttttacacaaaaaactgatacattcttatggatgtatctctacttttgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT
 || ||  | || | | ||    |   |     |  ||  |  | |||    |   || ||      |   ||  |   || | |  ||||| ||     || | |||||||||||||| ||||||||||||||  | || || ||||||||    |||    |  ||||  |||| || || || || || |  |||||  
gtaccatctcttctcatgattcaatccaaagattgtctctttttgttttgttatgcaattg------ttcaataaagagat-tgtctttttgttt-----agGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTCAATTCACGTCTTATTGCTGCTGATTATCTTGAATCCAACATTGATCTTA

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|148990860|gb|EE032278.2|EE032278

EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA

EST: gi|148951718|gb|EC897471.2|EC897471

EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA

EST: gi|5895978|gb|AW037224.1|AW037224

EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA

EST: gi|50339179|gb|CO534305.1|CO534305

EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA

EST: gi|74238607|gb|DT646521.1|DT646521

EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGANCAACA-GT
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGA-CAACAAGT

EST: gi|60352002|gb|DN218975.1|DN218975

EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA

EST: gi|148982842|gb|EE028691.2|EE028691

EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCCAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGAACA-CAAGT
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGA-CAACAAGT

EST: gi|149081164|gb|EE170272.2|EE170272

EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTA

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: 236

AGAGCCTGTAACTGAAGCATGTGTGCAACTGACCCAAGAATTCTTCAGGGAGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tacacaaaaaactgatacattcttatggatgtatctctacttttgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT

     aaaaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcaagtatttgaagaccggagggagtacctcccttgtcctttttacacaaaaaactgatacattcttatggatgtatctctacttttgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT

- - - - - - - - - - - - - - - - - - - - - - - - -caaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggatg