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

...atatcattgataccttggtcttgtatgatattgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgccctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA

Basic information

species	Zea mays
transcript	GRMZM2G177001_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 5

-atatcattgataccttggtcttgtatgata-ttgatcacttcagttctgaaatttcatgaccagttacacaaatct-aacatgccctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA
       |   ||  |||   |  |||  ||  || |  ||| |  | |||| |||||       ||||| | ||||  |  ||||||| ||  |||||| ||||||||||||| || |||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| |||||||| ||  | ||||| ||||  |
agccagctccttaagttgtattaatatattagctgtttcctttatgtttgaattttcacagttgattacatagatcttgatgtgccctgatc--ttttgt-agGGTTCAAGTGTACCTTTGGTTGTTAAATGGGCTGACACTGAGAAGGAAAGACAAGCTCGAAAAGCACAAAAGGCTCAATTTCACCCATCTAATATGTCAA

upper sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5

atatcattgataccttggtcttgt--atgatattgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgcc-ctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA
 |||  ||     ||    | ||   | |  | ||||      |  ||   || |  || |  | | | | |  |  || |||    | ||  | ||   |||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||||| ||| || ||||| || | |||  |||||||  |     
-tatgtttctccactcatacatgacaaagtcactgatattgctaactcgacaagtatatta--attcagatatttgcaatatgatatttgttgtcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC

upper sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 5

atatcattgataccttggtcttgtatgat-attgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgcc-ctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA
|| |  |  |  | |   |     |   | | ||||      |  ||   || |  || |  | | | | |  |  || |||    | ||  | ||   |||| ||| ||||||||||| ||||||||||||||||| ||||||||||||||||| ||||| | ||| || ||||| || | |||  |||||||  |     
atgttctccactcatacatgagagaaagtcactgatattgctaactcgacaagtatatta--attcagatatttgcaatatgatatttgttgtcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC

upper sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4

atatcattgataccttggtcttgtatgatattgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgccctggtcatttttgtt-----agGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA
     | | |||| | | |      ||  | | |       |  ||    |||  || |  | | | |||| |  ||  ||   |||| ||||||  |     |||||||||||||||| ||||||||||||||||| || ||||||||||||||||  |||||||  || |||||||| || | |||   ||||||||||  | 
tagctactcatacat-gatgaaaattgtcaattaaattgctaactcaatgattatataa--attcatacaattgcaatctga--tggttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC

upper sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 5

atatcattgataccttggtcttgtatgatattgatcact--tcagttctgaaatttcatgaccagttacacaaatctaac---atgccctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA
   |  ||  | ||| |||  | ||  || ||    |||  |   |  ||||| ||    |  |  |  |||| |  |     ||||     |    ||    |||||||||||||||| |||||||| |||||||| || |||||||||||||| |  |||||||  || |||||| | || | ||    ||||||   |  | 
---ttgttt-tgcctgggtggt-taatatgtttgctactcgtacatgatgaaaattgtcaattaagttgacaattgcagtctgatgcttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC

upper sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G03110.1 (Arabidopsis thaliana), 3'ss of exon 5

atatcattgataccttggtcttgtatgatattgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgccctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCA-GTCTTCTAACATGTTGA
          ||  |    ||| |   |  ||||  ||||    | || || |   |     |  |     |||     |    ||||  || || ||||||||||| |||||| || |||||||||||||| ||||| |||   ||||| ||  |  ||| |   ||||| |||||||  ||  ||  |  || |   ||
---------gtaatt---gcttttgctactttgaaaacttaccgtttgtaaatctgtagtgtgaaaattccatcatttttcttttggtt-ttcttcttagGGTTCAACTGTTCCTTTAGTTGTCAAATGGGCAGACACAGAACGAGAAAGACACACAAGAAGACTTCAAAAGGCTCAATCTCACATCGCCCGAC-TAGGGA

upper sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5

--atatcattgatacct-tggtcttgtatgatattgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgccctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCA-GTCTTCTAACATGTTGA
  || |  ||  ||| | |  |  | |   | |||  |    |    |    | ||  |||   |||   |||| | | |||| |  |  |  || || ||||||  ||| |||||| ||| |||| |||||||| ||||| ||||||||||| || ||||||| |   | ||||| |||||  || |||| |  ||  | |  
gtatgtgcttattacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaa-tatcacattctttttttcttctt-ttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC-

upper sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 5

atatcattgataccttggtcttgtatgatattgatcacttcagttctgaaatttcatgaccagttacacaaatc-taacatgccc--tggtcatttttg--ttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA
   ||     | |  ||   | | ||  |   |||  || |  |    ||||           ||  |  | |  | |  || ||  | ||   | |||  ||||||||||||||||||  | ||||||||||||||||| |||||||||||||| || ||||| || || || ||||||||||  ||| | |||||  ||   |
---tccccagttctgtgaagtgggatagtg--gatttctgccttataaaaatggagaagttgattcgatgattggttatctgaccattagtttctgttgcattagGGTTCAAGTGTTCCTCTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGGAAGGCTCAGAAAGCTCAATCTCAGGCATCTAATTTGCCAA

upper sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S175_12V6.1 (Physcomitrella patens), 3'ss of exon 6

atatcattgataccttggtcttgtatgatattgatc-acttcagttctgaa--atttcatgaccagttacacaaatc--taacatgccctggtcatttttgtta----gGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA
              |||      ||   | ||  ||   ||||  |   ||  |||  |||| || |  ||    ||  ||| | || |||   ||  | | ||    ||||||      | | ||||| |||||||||||||||||||| || ||||||||||| || ||||  || || ||||| |     ||||||  |    |  
---------gcgttttgtatgattactgtgttcttctggttcatgtgcaaataattaaatgaacaatcgcagcggtccataataagcactgacgatgatcgctattcagGGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGGCAGGCGCGTAAAGTGCAGAAGGCTCAGTCGGTTTCTTCTCCCCCCATTC

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|149108797|gb|EE189842.2|EE189842

EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG

EST: gi|60400937|gb|DN233744.1|DN233744

EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG

EST: gi|149098711|gb|EE184722.2|EE184722

EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG

EST: gi|71438922|gb|DR819972.1|DR819972

EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG

EST: gi|211051931|gb|FL422541.1|FL422541

EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG

EST: gi|89761503|gb|DY689493.1|DY689493

EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG

EST: gi|60396221|gb|DN229090.1|DN229090

EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCA
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCA

EST: gi|6020453|gb|AW065381.1|AW065381

EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG

EST: gi|6564129|gb|AW231751.1|AW231751

EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTT
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTT

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), 46 (downstream exon)
Score: 67

CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA

Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 33

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 17

Block sizes: 45 (upstream exon), 39 (downstream exon)
Score: 14

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaatttcatgaccagttacacaaatctaacatgccctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA

                          atctaac  putative branch site (score: 14)
                                          tcattttt  putative PPT
                                            atttttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatcattgataccttggtcttgtatgatattgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgccctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - ttgtatg
- - - - - - - - - - - - - - - - - -cacttca
- - - - - - - - - - - - - - - - - - - - - -ttctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - -tttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgccc