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

...tttagaagttacatggacacacttgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgacttgaactgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT

Basic information

species	Zea mays
transcript	GRMZM2G415007_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 4

tttagaagttacatggacacacttgcttttagt--gttgagcacatttcctgtgagcttgcat----atctatttctgacttgaactgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
|||  || | |        |  |||   |||||  || |     |||  ||| ||   ||||     ||  || | ||||| ||||||| ||| |||||||    |||||||| ||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
ttttaaactaatgacatgccttttgtagttagttggtcgtcttgattatctg-gatagtgcactgtgattcatatttgact-gaactgtctcatctcttca----gGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 4

------tttagaagttacatggacacacttgcttttagtg---ttgagcacatttcctgtgagcttgcatatctatttctgacttgaactgtatcacctcttcatt--cagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
        |   |   ||||  |||||   |  |  | ||   ||    |   || |  | |  ||   | |||  | || |  |   || | ||   |   | ||   ||||||||||||||| || || || ||||| |||||||| || ||||||||||| ||| |  | ||||| ||  ||||||||||| | || |||||||||||
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4

---------------------tttagaagttacatg---gacacact-tgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgacttgaactgtatcacctcttcattc-agGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
                        | ||| || |||   |  |  || ||    |    ||    |   || |  | |  ||     | | || || |  |   || |      ||  | ||| ||||||||| ||||| ||||| || ||||| |||||||| || ||||||||||| ||| |  | ||||| ||  ||||||||||| | || ||||| |||||
gtgagtacttttatacacatacacacaagcta-atgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 4

----------------tttagaagttaca-tggacacacttgcttttagtgttgagcacatt-tcctgtgagct---tgcatatctatttctgacttgaactgtatcacctcttcatt--cagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
                ||||  |||   | |    | |  |  || |   |   |  | ||| | || |   |    | |   |||  |  | |      || | || |||   | ||  |||||||||| ||||| ||||| || ||||| |||||||| || ||||||||||| ||| |  | ||||| ||  |||||||||   | || ||||| |||||
gtgagaattttttttttttatgagtcttaataagaagaacttattatgtagaaaaatatattattctttccaccaaattctcctctgatgttaatgcttgctatgtctccttcgccttgccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAGTAGAGCACTTGGCAAGCT

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 4

-------------------------------------------------------------tttagaagttacatggacacacttgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgacttgaactgtatcacctcttcatt----------cagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
                                                             ||   | |  | ||| |   |  |     ||||    | ||  | ||      |   |  | | |   | |||  |     ||| |   |  |  ||          |||||||||| |||||||| ||| | ||||| ||||||||||||||||| ||||||||| ||   ||||||||| |||||||||||   |||||||| |||||
gtaatatacttgtgaccaggaatgaattgttttgaattgcattgtgttcaataacaaatgattgctatgcca-atgcaataagctaaacatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtggtaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGGTGATGGAGTACTTCATCAAGTTGATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4

----tttagaagttacatggacacacttgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgacttgaactgt-atcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
     ||  ||| ||     |  || |  | | |        | |    |  | | ||  || || |   |      |||    ||| || | ||       |||||||||| |||||||| ||||||||||| |||||||||||||| || ||||||||| ||   ||||||||| |||||||||||   |||||||| |||||
cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtg-atgttggtgctaaccttttgttgttatgatct----gcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4

tttagaagttacatggacacacttgcttttagtgttgagcacatttc--ctgtgagcttgcatatctatttctgacttgaa---ctgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
  ||||| ||||   | || |   |   | |      | ||  |||   ||   |   ||   ||| |||    | | |||    | | |    | ||  | |||||||||||||||| ||||| |||||||||||||||||||| ||||||||||||||| |  | ||||||||| ||||||||||| | ||| |||| ||| |
-atagaa-ttacggtggcaaatggg---tgaaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 4

--------------tttagaagttacatggacacacttgcttttagtg---ttgagcacatttcctgtgagcttgcatatc-tatttctgacttgaactgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
               |     | | |     ||   ||||| || |     |  |  | | ||   | |||      |||  || |   ||     |  ||   |    ||| | ||||||||||||||||||||||||| ||||| ||||| ||||||||||| ||||||||| || | ||||||||| ||||||||||| | |||||||| |||||
GTGAGGATTTTTTTCTCTACTGATGCTCTTTCATCTTTGCTCTTTGCACATTGAAAGAAAATTTACGAGAGGAAAGTTATTATACTGTGGATGCTCAAGGTTCAATTCTTTCCTGCAGGTGAGGATTTTGACCAGAGGATTATGGAGTACTTTATCAAGTTGATTAAGAAGAAGCACGGAAAGGACATCAGCAAGGACAACAGAGCTCTTGGGAAGCT

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4

tttagaagttacatggacacacttgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgac--ttgaactgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
                                      | || ||         |||     | | ||||| ||   |  |   || || ||    || |||||||||| || || |||||  | ||||| |||||||||||| | |||||||||||| ||| |||||| ||| ||||||||||||| ||||||||||||||
--------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT

upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 4

tttagaagttacatggacacacttgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgac--ttgaactgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
                                      | || ||         |||     | | ||||| ||   |  |   |  || ||    || |||||||||| || || |||||  | ||||| |||||||||||| | |||||||||||| ||| |||||| ||| ||||||||||||| |||||||| |||||
--------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactgacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGCAAGCT

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|149067539|gb|EE157747.2|EE157747

EST:     CTGGCCACCAATGGTGACACCCATCTTGGAG                         GTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
genomic: CTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA

EST: gi|211197978|gb|FL446530.1|FL446530

EST:     GTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAG                         GTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
genomic: GTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA

EST: gi|67031277|gb|CO460026.1|CO460026

EST:     TA-CGGTGTGTTTGAGGTGCTGGGCACCAATGGTGACACCCATCTTGGAG                         GTGAGGATTTTGACCCAGAG-ATCATGGAATACTTCATCAAGTTTGATCA-
genomic: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACC-AGAGGATCATGGAATACTTCATCAAGTT-GATCAA

EST: gi|67043231|gb|CO469486.1|CO469486

EST:     TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAG                         GTGAGGATTTTGACCAGAGGATCATGGAATAC
genomic: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATAC

EST: gi|32849239|gb|CD988920.1|CD988920

EST:     TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAG                         GTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
genomic: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA

EST: gi|211430777|gb|FL361062.1|FL361062

EST:     TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAG                         GTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
genomic: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA

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: 198

GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT

Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 140

Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 174

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 761

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcctgtgagcttgcatatctatttctgacttgaactgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT

                      ttctgac  putative branch site (score: 761)
                                       tcacctcttcattc  putative PPT
              atatctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagaagttacatggacacacttgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgacttgaactgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - -catggac
- - - - - - - - - -cacttgc
- - - - - - - - - - - - - - - - - - - gcacatt
- - - - - - - - - - - - - - - - - - - - - - -tcctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtatc