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

gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA

Basic information

species	Zea mays
transcript	GRMZM2G152127_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 8

gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttat---acatttttgggggcatccttgcgagaaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA
                                                                                | ||||| |  |||||| | ||    | | ||||  || ||||     ||| ||| || ||| |||| |||  | | |      |  || |||||| ||||  ||||||||| |||| |||| |||||||||  | ||| |||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||  |||
--------------------------------------------------------------------------------cctgtttct-gtttcaactctacaaaataattttatggacatca----gagcaatgtgactttatat-tcatctggtattaagataattatctgttttacctgcagGGAGGTGAAGAAAAGTATGAACTTCCTACAAAGCAAAAGGATGATATCTGTACAATAATGTACACCAGTGGAACAACTGGTGACCCTAAGGGAGTTTTAA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 8

gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaata--tgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA
                                                                                  |   | |||  ||| |      ||      |     |  ||  |   | ||  ||  || || | ||| ||    | |    |||||  |||      | |||||   |||  |||  ||||| |||||    ||  ||||   |||  | |||||||||||||| || |||||||| ||||||||||| ||||||||  | |
----------------------------------------------------------------------------------taactctcagctcagaaaaggccaaggaaagcaatgtgtttatggatattaactggtttcatttctca-ttcctcattccagtttttgatgtctag--agcagGGTCATAATCAGAGTTTTGATCTTCCTGTTAAAAAAAAAAGTGATGTGTGTACAATAATGTATACAAGTGGAACTACTGGTGATCCCAAGGGAGTTTTGA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G43470.5 (Glycine max), 3'ss of exon 8

gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA
                                                                      |   || || ||||   |   ||  || |   ||  | |||    || || |||        ||   |||   |  |  ||   || | |||||||      ||| ||| |||||    ||  |||  ||||| |||||    ||| ||| |  |||||| |||||||||||||| || |||||||| |||||||| || ||||||||  | |
--------------------------------------------------------------------gttaatttcagtcatgacctc--ttggaagtaattatgtcttt---tgcttctttgg-------atattttgtggttcccattcctaattcattttttaat--atctgcca-cagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 8

gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA
                                                                              |   |   ||||| |    |  | ||    ||           ||||    |||||   ||  | | ||   |    ||||   |||||  | | || ||| |||||    |   |||  ||||| |||||    ||| ||| |  |||||| |||||||||||||| || |||||||| || ||||| || ||||||||  | |
------------------------------------------------------------------------------gaggttaatttcagtcatgacctctaggaattaattatgtcttttgctttgaatat---tttgtgtttcccattcctaattcaatttttaatat-ctgcca-cagGGTCAAACTCAGAGCTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACCGGTGACCCCAAGGGAGTGTTGA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G02620.1 (Glycine max), 3'ss of exon 8

gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA------------------------------------
                                                                                                                                                                            ||||  | |||||   |||  |||  ||||| |||||    ||  | ||   |||  | |||||||||||||| || |||||||| || |||||||| ||||||||  | |                                    
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------gtctag-agcagggtcataatcagagttttgatcttcctgttaaaaagAAAAGTGATGTGTGTACAATAATGTATACGAGTGGAACTACAGGTGATCCCAAGGGAGTGTTGATAACCAACGAAAGCATTATTACACTCTTAGCTGGGA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G64400.1 (Arabidopsis thaliana), 3'ss of exon 8

gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaatatgccttgatatatcagttag-aaaattatt--ttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA
                                                                                                              |  |   ||| |       | | | | || | ||   | |||  ||||| ||   | | |  |  |  |     |||| |      |  | | |||| | |||   |||   |     ||  | || || |||||||| || ||||| ||||||||||||||||| |||||| |  
-------------------------------------------------------------------------------------------------------------gtaagaaaatcat-atttttattctactttaacatcagaattatcaaaatcatgaatatatattacttaatttgaagGGCGAGGGTAAACATTATGAATTACCAGAGAAGAGGAGAAGCGATGTTTGCACCATAATGTATACAAGTGGCACAACTGGTGATCCTAAAGGAGTATTGC

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 8

gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA
                                                                                  | || | |||||      | |  ||| || |   | |  ||   | | ||     ||    |||     ||  ||   || | ||| |||| | |  |||||||| | |  | || ||||| ||||||   |   | ||  | ||||| ||||||||||||||||| ||||||||||| ||||| || || || ||  | |
--------------------------------------------------------------------------------agttttctgcatttttc-cctctttattgttagatacctatttataa-acatgctattttgcctatagaaaagttaaagcttgtgtttttgtt-tgctcacagGGAGATGATAAAAAATTTGATCTTCCATTGACAAAGAAAAACGACATTTGTACAATAATGTACACAAGTGGAACAACCGGTGACCCCAAAGGTGTGATGA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S113_124V6.1 (Physcomitrella patens), 3'ss of exon 8

gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA
                                         || ||     |||||   | |      |  ||  | |  |     ||| ||  || |||  ||  ||| ||     ||  ||  ||     |   ||  || | | | |     |  | ||| |    ||    |    ||||||   ||  |       ||  |  ||||      ||     || || |  ||||| |||||||| ||||| ||||||||||| || |||||||||||  
----------------------------------------gtaggtttcatgttacccaatt-----catcgtccttaatc----ctttgataacatattagtaattttatg-----atatttaagacgtggaattctacatttctgaatgtagcagctctttgtgaaatgggtgattttcagGGAAAGAATAACCCAACAGACTTAACACCTCCAACAACATCAGATATTTCCACAATTATGTACACTAGTGGCACAACTGGTGAACCCAAGGGAGTACTCT

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|91055766|gb|EB166184.1|EB166184

EST:     TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTG                         GGAGGTAAAGAGAAGTTTGAACTTCCCCCCAGGGAAA-GGATGACATATGT
genomic: TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT

EST: gi|76014959|gb|DT942129.1|DT942129

EST:     TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTG                         GGAGGTAAAGAGAAGTTTGAACTTCCACCCA-GGAAAAAGATGACATATGT
genomic: TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT

EST: gi|32867927|gb|CF007609.1|CF007609

EST:     TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTG                         GGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT
genomic: TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT

EST: gi|74239653|gb|DT647567.1|DT647567

EST:     TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCCACTG                         GGAGGTAAGGAGAAG
genomic: TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAAG

EST: gi|71426983|gb|DR808033.1|DR808033

EST:     TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTG                         GGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT
genomic: TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT

EST: gi|148958182|gb|EC904386.2|EC904386

EST:     TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTG                         GGAGGTAAAGAGAAGTTTGAACTTCCACCCCAGGAAAAGGATGACATATGT
genomic: TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT

EST: gi|76011816|gb|DT938986.1|DT938986

EST:     TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTG                         GGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT
genomic: TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT

EST: gi|148961536|gb|EE012289.2|EE012289

EST:     TGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTTCTGCA-CTG                         GGAGGTAAAGAGAAAGTT-GAACTTCCACCCAAGGGAAAAGGATGA
genomic: TGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTT-CTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAA-GTTTGAACTTCCACCCAAGG-AAAAGGATGA

EST: gi|24766862|gb|CA402007.1|CA402007

EST:     TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTG                         GGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT
genomic: TTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGT

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), 47 (downstream exon)
Score: 147

CACTTGTAAGCTTCGGTAAGGTTGATCCTGGGCACAAGGAAAAAGTTGAACAGAATGGCTTGTCCATCTACTCATGGGAAGAGTTTCTGCAACTGgtaaggttct ... ctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 101

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 47

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 209

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA

       ccttgat  putative branch site (score: 209)
                             ttattttttttctgtt  putative PPT
         ttgatatatcagttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA