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

...ctatatgtgaatatgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC

Basic information

species	Zea mays
transcript	GRMZM2G108115_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g52340.1 (Oryza sativa), 3'ss of exon 2

--ctatatgtgaatatgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
  |||| |       | |||      ||| |   |  ||||    |  ||  ||  ||    |||       | | | || | ||  | |||   | || |||||||||||||||||||||||||||| ||||| ||||||||||||||   |||||| ||||||||||| |||||||| || ||||||||||| ||||| |
gactattttatttgttaactttgtgtatgattgcaccaaaatatgacattgaaaataaacactcaaaaaaattcacttgtttatt--tgctttcttgtttagGTTAAATTGTGGTGTGACTGCCCTTTCTGGCCTGATGATGGAATGTGTCGGCTTAGGGATTGTAGTGTCTGTGAGTGCCCAGAGAATGAGTTTCCTGAGC

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G23150.1 (Glycine max), 3'ss of exon 2

ctatatgtgaatatgactaccaaaatgc--tcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
 ||| |  |||||    || | ||||||  |  | ||  |  |    |         ||| ||| ||||| ||||    |  || | |     | |||  |||| || || ||||||||||||||||| ||||| |||||||| |||||   | |  | || |||||||| ||||| || || || ||||| ||||| ||| 
-tatgttggaatactgataactaaatgcatttctttttcacttttgttgaccctctcatgtttcttctgtgctaaagacta-gtgggtgaaattttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 2

---------ctatatgtgaata-tgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
          ||| | |||||| |||  || ||| |||   | ||   | |    ||      || ||  || ||||| ||||     |||    |  || |      |||| || || ||||||||||||||||| ||||| |||||||| ||||||  | |  | || |||||||| ||||| || || || |  |||||||| ||| 
tcatgcattatatgtttgaatactgataactaaattgcatttcttttcacttttgttgaccctca-tgaatcttctgtgctaaag---gtgaaactttttat------agGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G72280.1 (Arabidopsis thaliana), 3'ss of exon 2

ctatatgtgaatatgactaccaaaatgctcatattaaaaa----taaaatt----tttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtctttta---agGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
   |  ||||  |||  |   ||   | | || |  ||||    | || ||    | |      | |||  |   || |   | |    || ||  ||   | ||    |||||||| | |||||||||||||| || ||||| || |||||||||||     |  | ||||| ||||| ||||| ||||| ||||||||||| || ||||
--gtcagtgag-atgctttagaatccgattatgtcgaaaaactatgaagttgtgttctgtagtgtagttagtgacttttggctggctgttttttttttaaatgttgggtagGTTAAACTATGGTGTGACTGCCCATTCTGGCCAGACGATGGAATGTGTCGTTTGCGTGATTGCAGTGTCTGTGAATGTCCAGAGAATGAGTTTCCAGAAC

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 2

ctatatgtgaatatgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
              |       | ||       || |  || ||| | |  ||  | | ||     ||     ||  |  |||       || |  || ||||||| |||||||||| ||||| |||||||| |||||||| ||||||  | | ||||| || ||||||||||| ||||| || |  |||||||||||| 
--------------gttggttcatatttcttctttgatcatgaaagtatctag--aggatttggaggtgtgttgtgataggtttgaatgcgtttaata-gGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0027g00090.t01 (Vitis vinifera), 3'ss of exon 2

ctatatgtgaatatgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtctttta--agGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
  | ||   ||| | | |      ||     |  |     |  |||  || | || | |||     ||||   |  |  || ||||| |  || |     |||||||  |||||||| |||||||||||||||| |||||||| |||||||||||  | ||||| ||||||||||| ||||| || | ||| || || ||||
--aaattcaaatgttattttatctatatatcttctttgtttggaatgctttatcacttgtttccgagttccttggagcctgatgttcttgttcctaaggcagGTTAAGCTGTGGTGTAACTGCCCTTTTTGGCCTGATGATGGTATGTGCAAGCTGCGTGATTGCAGTGTTTGTGAATGTCCTGAAAGTGAATTTCCAGAAC

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 2

--ctatatgtgaatatgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtctttta-agGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
   | |||     ||| ||| | |      |  | ||     | |  |  || |   |    |   |  || |  |  |  ||||| ||| | ||| |   ||| ||| |||||||||||||||||||| ||||  |||||||| |||||| |  |  | ||||| ||||||||||| || || || ||||||||||||||| 
ttgtttattctgttat-acttcaattgatattgtgttttcgctta--tgcttgactgacctatatcccattttctgaagcctgttgatccatttctatggtagGCTAAGTTGTGGTGTGACTGCCCTTTCTGGCTAGATGATGGTATGTGCCACTTGCGGGATTGCAGTGTTTGTGAATGCCCCGAAAATGAGTTCCCTGAAA

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|24764810|gb|CA399972.1|CA399972

EST:     ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAG                         GTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG
genomic: ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAGgtgagcagtt ... gtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG

EST: gi|211489776|gb|FL012897.1|FL012897

EST:     ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAG                         GTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG
genomic: ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAGgtgagcagtt ... gtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG

EST: gi|149060174|gb|EE157144.2|EE157144

EST:     ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAG                         GTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG
genomic: ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAGgtgagcagtt ... gtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG

EST: gi|32865873|gb|CF005555.1|CF005555

EST:     ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAG                         GTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG
genomic: ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAGgtgagcagtt ... gtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG

EST: gi|211489777|gb|FL012898.1|FL012898

EST:     TCCAATCCTACAGGAACTCGTTAAGTTGCCMCTTCTTCAGGTACTTCAAG                         GTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG
genomic: TCCAATCCTACAGGAACTCGTTAAGTTGCC-CTTCTTCAGGTACTTCAAGgtgagcagtt ... gtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG

EST: gi|50338345|gb|CO533471.1|CO533471

EST:     ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAG                         GTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG
genomic: ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAGgtgagcagtt ... gtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG

EST: gi|211489775|gb|FL012896.1|FL012896

EST:     ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACYTCAAG                         GTTAAATTGTGGTGTGACTGCCCTTTTTG
genomic: ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAGgtgagcagtt ... gtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTG

EST: gi|31363511|gb|CD447868.1|CD447868

EST:     ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAG                         GTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG
genomic: ATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAGgtgagcagtt ... gtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAG

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: 44 (upstream exon), 48 (downstream exon)
Score: 34

CTGCTGCTGCGACTATGAGACGGTGGACGCCATCAACGAGGAGGTCCTGCATCCAATCCTACAGGAACTCGTTAAGTTGCCCTTCTTCAGGTACTTCAAGgtgagcagtt ... gtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC

Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 121

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 51

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC

                                    ttgttccttgtctttt  CT-rich tract
                                              tcttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatatgtgaatatgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - -aatgctc
- - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttcatc