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

...tgctgatgcttccaagtttatcttcttgtaactataggttacctttttctgttttcttataatctgtaggcttaactctgtaggctcccatgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG

Basic information

species	Zea mays
transcript	GRMZM2G153722_T01
intron #	10
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g34950.1 (Oryza sativa), 3'ss of exon 10

tgctgatgcttccaagtttatcttcttgtaactataggttacctttttctgttttcttataatctgtaggcttaactctgta---ggctcccatgttttt-cagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG
       | ||   ||     ||  |   |  ||| |    ||  |  | |  |||     ||||       | ||||  ||      ||   |  | ||  ||||||| ||||||||||| || || |||||||||||||| |||||||||||||||||| ||||  | ||||| ||||||||||||||||||||||||||||
----agggtttatgagacaggctgataagatttattgcaggccagtagcagcattcgatatatcttctcatatgactcattaatgaagtcttgtcctcttgtagGGAATTGATGTGATGGATTACTCATTGCTTGTGGGAGTTGACGAGGAGAAACATGAATTGGTTCTGGGAATAATTGATTTTATGAGGCAGTATACATGGG

upper sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G05000.1 (Glycine max), 3'ss of exon 14

tgctgatgcttccaagtttatcttcttgtaactataggtta-cctttttctgttttc-ttataatctgtaggcttaactctgtaggctcc--catgttttt-cagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG
  || |    | |    |||   ||  ||     ||  ||| |||     ||  ||  ||| | |   || |    |  |  ||   |    ||| || || |||  |||  ||||||||||||| || ||||| || ||||| || ||||| || ||||| ||||| ||||| || ||||||||||||||||||||||||||||
--ctaacatattc---cttaaaatcaagtgggagtatattagcctccagatgcattaattagagtgcatatgaaacatccattaatattgtacatattgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGAGTGGATGAGGAAAAGCATGAGCTGGTTTTAGGTATCATTGATTTTATGAGGCAGTATACATGGG

upper sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA16G01590.1 (Glycine max), 3'ss of exon 12

------------tgctgatgcttccaagtttatcttcttgtaactataggttacctttttctgttttcttataa--------------tctgtaggcttaactc-tgtag----gctcccatgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG
               | ||   |   | | |  |||||  ||||| |    |    || | | |||||||  ||              ||| || |   | |||   ||     | |  | | || | |||  | | ||||||||||||||||| || || || ||||| || || || || |||||  ||||  | ||||| |||||||| |||||||||||||| ||||
gtaaatctcaaaactttatatgtggcattcttccttctcttaactgtctccttttcttgtttcttttcttgcaaagtgcacatcatcatctttatgtccatctcacataaatctgttttcctcttgtgcagTCAGTTGATGTGATGGACTATTCTTTACTGGTTGGAGTGGATGAAGAAAAGCATGAGTTGGTTATTGGAATCATTGATTTCATGAGGCAGTATACTTGGG

upper sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G05100.1 (Glycine max), 3'ss of exon 11

-----tgctgatgct-tccaagtttatcttcttgtaactataggttacctttttctgttttcttataatctg--------taggcttaactct-----gtaggctcccatgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG
     |  | |   | ||   |    ||||  |     ||   ||  ||||||||| || |   | |||           || | | | |||       |  | |  | | || | |||  | | | ||||||||||||||| || || || ||||| || || ||||| |||||  ||||  | ||||| |||||||| |||||||||||||| ||||
gtaagtcttaactttatctgtgacattctttcttctcttaactgtctcctttttcttttcttgcaaaatgcacaccatattatgttcatctcccatgaatctgttttcctcttgtgcagTCAGTTGCTGTGATGGACTATTCTTTACTGGTTGGAGTGGATGAAGAGAAGCATGAGTTGGTTATTGGAATCATTGATTTCATGAGGCAGTATACCTGGG

upper sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G17510.1 (Glycine max), 3'ss of exon 10

---tgctgatgcttccaagtttatcttcttgtaactata--ggttacctttttctgttttcttataatctgtaggcttaactctgtaggctcccatgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG
        |    |   ||| |||   | |  || |  |   ||||   ||   |||     || ||  |  |   ||||   |||        || | || |||  |||  ||||||||||||| || ||||| || || || || ||||| || |||||  |||| ||||| || ||||||||||||||||||||||||||||
cctaaaaaacaagtgggagtgtattagcatccaaatgcattagttagagttca-tgtgcctgtaaaacatcca---ttaatattgtgcatattgat-tgttgcagTCAATATATGTGATGGACTACTCATTGCTGGTTGGCGTGGATGAGGAAAAGCATGAGTTGGTTTTAGGTATCATTGATTTTATGAGGCAGTATACATGGG

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|5268767|gb|AI770731.1|AI770731

EST:     CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCT                         GGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA
genomic: CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA

EST: gi|166590491|gb|EG201272.1|EG201272

EST:     CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCT                         GGAATCGATGTGATGGACTATTCCTTGCTTNTGGGA
genomic: CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGA

EST: gi|26456235|gb|CA827818.1|CA827818

EST:     CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCT                         GGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA
genomic: CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA

EST: gi|211056608|gb|FL029990.1|FL029990

EST:     CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCT                         GGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA
genomic: CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA

EST: gi|211056609|gb|FL029991.1|FL029991

EST:     CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCT                         GGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA
genomic: CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA

EST: gi|20208322|gb|BQ134411.1|BQ134411

EST:     GGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCT                         GGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA
genomic: GGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA

EST: gi|6601646|gb|AW256042.1|AW256042

EST:     CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATAC-TCTTTCCTAGCT                         GGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA
genomic: CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA

EST: gi|241994780|gb|GR421133.1|GR421133

EST:     CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCT                         GGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA
genomic: CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA

EST: gi|84980314|gb|DW530663.1|DW530663

EST:     CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTNTCCTAGCT                         GGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA
genomic: CAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAA

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: 46 (upstream exon), 48 (downstream exon)
Score: 149

GAACTTAATTGAAGCAATGCCAACTTCACCGATTTTTGTTGGGAACAAGGCAAAGCGGCTACTGGAAAGAGCTGTTTGGAACGATACATCTTTCCTAGCTgtaagtttgc ... tgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 106

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttctgttttcttataatctgtaggcttaactctgtaggctcccatgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG

                        gcttaac  putative branch site (score: 106)
                                       ctcccatgtttttc  putative PPT
      ttttcttataatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgatgcttccaagtttatcttcttgtaactataggttacctttttctgttttcttataatctgtaggcttaactctgtaggctcccatgtttttcagGGAATCGATGTGATGGACTATTCCTTGCTTGTGGGAGTCGACGAGGAGAAACATGAACTGGTCTTAGGAATTATTGATTTTATGAGGCAGTATACATGGG

-gctgatg
- - - - - - - - - - -cttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctccca