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

gtttgatgaagatcctcacttatatatgtatcgatcttattgctagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT

Basic information

species	Zea mays
transcript	GRMZM2G105019_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 8

gtttgatgaagatcctcacttatatatgtatcgat-cttattgctagaacttgggtttatcgaatatgaatggggtttcatga-tttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT
  ||  | | ||| | ||    |  | || ||  | | | | |  |   ||||   |    |   || | ||   |  ||||| ||||  | | || ||||||||||| || || ||||| || |||||||||||||||||||| ||||||||||||||||  |||||||||||||| |||||  | || |||||||| |
-gttagt-atgatgcacatggttcaacgtttcactgcctgtggacattccttgaactc--tggtaattattgaattgccatgactttgaatttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGTGACATCTACAGTGATGCTGATGAAGACATGCGACGAGCAATGATGAAAT

upper sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G37440.1 (Glycine max), 3'ss of exon 9

gtttgatgaagatcctcacttatatatgtatcgatcttattgctagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT
          | |  |||  | || || |||  |   | ||  |      | ||||  |   |  |   |    | || | |      |     ||||||||| |||||||||||||||||||||||||| ||||||||||| |||||||| || ||  | ||||| ||||| || |   | || || ||||  || |
----------gtttgtcagctctacatatataaaatgtttttgttctttgtaggttggt-acacttccttcccctatcctaacac---ttcatttcagGAGAAAGAAGAAAAACTTGATGGTGATGCTGCGTTGAACAAATTTTTCCGTGATATATATCAAGATGCAGATGAGGACACAAGAAGAGCAATGAGCAAAT

upper sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 8

gtttgatgaagatcctcact-tatatatgtatcgatcttattgctagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT
           ||  |  || | | | |  |      | |||  | | | ||  ||   |  ||      | |    | |   | |   |     ||||||||| || ||||| |||||||| |||||||||||||||||||| ||||| || || ||  | ||||| ||||| ||||   | || || ||||  ||||
---------gtatgtttgctgtctttgtaaagtctcttaattctttgtattttagtgattgcaactc---ttgctcctaacattcttcattcatttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGT

upper sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G43150.1 (Glycine max), 3'ss of exon 6

gtttgatgaagatcctcacttatatatgtatcgatcttattgctagaac-ttgggtttatcgaatatgaatggggtttcatgatttgtg-tctgca--tcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT
      |  | |||   |   |      | |  | || | | |   | | ||  ||  | |   | | ||     ||     |  |||| |||||   ||||||||| |||||||| ||||||||||||||||| ||||| ||||| |||||||| || ||| |  |||| ||||| || ||| |||| || ||||  ||||
--agagtatacatcaagatcaaacagaatctgtacctcactacctcatcattttgtggaacatgtttaaacaatattgacgaaaatgtggtctgctattcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAATAAATTGTTCCGTGATATTTACCAAAATGCAGATGAGGACATGAGGAGAGCAATGAGCAAGT

upper sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G02340.1 (Glycine max), 3'ss of exon 6

--------------gtttgatgaagatcctcacttatatatgtatcgatcttattgctagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT
              | |  |  |  |||   || |   ||  |    || || |     |||| ||  | ||   |||||  |||    |   || | ||  | |    |||||||| |||||||| ||||||||||||||||| ||||  ||||| |||||||| || ||| |  |||| ||||| || ||| |||| || ||||  ||||
agagtatacatcaagatcaaacagaatctgtacctcactacctcataattttgt----ggaacatg--tctaaaaaatattgatgaaaat--gtggtctgccttt----cagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGTGATATTTACCAAAATGCAGATGAGGACATGAGGAGAGCAATGAGCAAGT

upper sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 8

gtttgatgaagatcctcacttatatatgtatcgatcttattgctagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT
|||||      ||| ||      |  ||| |  ||  | |||  |         |||| ||  |   | |      || | |  | | |     ||||||||| || ||||| |||||||| |||||||| ||||||||||| |||||||| || ||  | ||||| ||||| ||||   ||||||| ||||  ||||
gtttgcctgctatcttcgta---aagtgtgttaattct-ttgtaa---------tttaacggttgcaactcttagctcctaacat-tcttcatttcagGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGTGAAATATATCAAGATGCAGATGAGGATACAAGGAGGGCAATGAAAAAGT

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|148972746|gb|EE023715.2|EE023715

EST:     AAAGGCGAAAAAAGACTGGGATAAACT-GAGAGCTGAAGTCAAAAAGGAG                         GAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGT
genomic: AAAGGCGAAAAAAGACTGGGATAAACTGGA-AGCTGAAGTCAAAAAGGAGgtttgatgaa ... tctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGT

EST: gi|67031272|gb|CO460021.1|CO460021

EST:     CAAAGGCGAAAAAAGACTGGGATAAACTGGGAGCTGAAGTCAAAAAGGAG                         GAGAAGGAAGAANNNACT-GATGGTGATGCTGCATTGAACAANTTNCT-C-
genomic: CAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAGgtttgatgaa ... tctgcatcagGAGAAGGAAGAAAA-ACTTGATGGTGATGCTGCATTGAACAAATT-CTTCC

EST: gi|5005807|gb|AI711869.1|AI711869

EST:     CAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAG                         GAGAAGGAAGAAA
genomic: CAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAGgtttgatgaa ... tctgcatcagGAGAAGGAAGAAA

EST: gi|113681984|gb|DW840964.1|DW840964

EST:     CTGAAGTCAAAAAGGAG                         GTAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCG
genomic: CTGAAGTCAAAAAGGAGgtttgatgaa ... tctgcatcagG-AGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCG

EST: gi|8383133|gb|BE056076.1|BE056076

EST:     CAAAGGCGAAAAAAGACTGGGATTAACTGGAAGCTGAAGTCAAAAAGGAG                         GAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGT
genomic: CAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAGgtttgatgaa ... tctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGT

EST: gi|6056546|gb|AW090936.1|AW090936

EST:     CAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAG                         GAGAAGGAAGA
genomic: CAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAGgtttgatgaa ... tctgcatcagGAGAAGGAAGA

EST: gi|6031470|gb|AW076372.1|AW076372

EST:     CATAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAG                         GAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGT
genomic: CAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAGgtttgatgaa ... tctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGT

EST: gi|32857112|gb|CD996793.1|CD996793

EST:     GACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAG                         GAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGT
genomic: GACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAGgtttgatgaa ... tctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGT

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: 519

CTGAAACAGCCCCAAGACCTTCATACCCATCTTCAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAGgtttgatgaa ... tctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 568

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 664

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT

                  aatatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatgaagatcctcacttatatatgtatcgatcttattgctagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA