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

...tagtaacacttggtgtgttttcctcctgctgcatataactcttaatgcatttaagtttctgtttttttgtctgttcctgtaatccttgaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT

Basic information

species	Zea mays
transcript	GRMZM2G063511_T01
intron #	5
splice site	3'
intron type	U12 (go to U12 genes for details)

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 5

tagtaacacttggtgtgttttcctcctgctgcatataactcttaatgcattta-agt-ttctgtttttttgtctgttcctgtaatccttgaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT
  |||||  ||  | |||||||||  || |   ||| |    | |    |||  |||  ||| |||| ||||  ||| |||| |||||| |||    || |||||||||||||||||||||||||||||||||| || || |||||| |  | ||||| |||||||| ||||||||||||||||| || || ||||| || |
--gtaactatttttttgttttccttttgatcactattatggatcacaattttgtagtactctattttgttgttggtttctgtcatccttaaccagctattagATGACAAACACTATCCAGAAGAAGTTCAAGGTTTCTTCAACCCAATTATTATACCAATCTTGCCCCTATCAATCACTGACCCTCTTCCTTATTGGTCCAT

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5

tagtaacacttggtgtgttttcctcctgctgcatataactcttaatgcatttaagtttctgtttttttgtctgttcctgtaatccttgaccgttca---tcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT
   |  ||||||    | |||      |  |       || ||        |  | |    ||||||  | ||  | |    ||||| ||   |     | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || |||||| ||   ||||||||  ||  ||| || |
-tattgcacttgaaa-gctttataaaggtggttgtctgcttttttcattcctgggctatcatttttt-atttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5

tagtaacacttggtgtgttttcctcctgctgcatataactcttaatgcatttaagtttctgtttttttgtctgttcctgtaatccttgacc---gttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT
   |  ||||||    | ||| |    |  ||      || ||        |  | |    ||||||  ||||  | | |  ||||| |     | |  | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || |||||| ||   ||||||||  |   |||||| |
-tattgcacttgaaa-gctttacaaaggtggctgtctgcttttttcattcctgggctatcatttttt-atctgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 5

---------tagtaacacttggtgtgttttcctcctgctgcatataactcttaatgcatttaagtttctgtttttttgtctgttcctgtaatccttgaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT
            || |  ||||| | |  |     |  | | |  | || |  ||  || |    ||       || |  || |  | |  |     |  || || ||||||||||| || ||||||||||||||||| || ||||| || || || || || ||||||||||| |||||| || | || || ||  ||| ||| || |
gtatcctatgcctagcctttggtttctcattgctttatt-ctttcacctttctatatatcttgtcttaaaccaattcga-tgctgttatcttaaccaattgtaca-cagATGACAAATACCATCCAGAAGAAGTTCAAAGTTTCATCCACGCAGCTTCTGTATCAGTCTTGCCCATATCAAGCAATCACTCTTTTCGTCACTGGGCCAT

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 6

--------tagtaacacttggtgtgt--tttcctcctgctgcatat-aactcttaatgcatttaagtttctgttttttt---gtctgttcctgtaatccttgaccgttcat---cagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT
        |  | | | |   | |    |||||   ||     ||| | |   |  | ||  ||| |    || ||| |       ||| |||| ||| || |||  | ||   |||||||| || || ||||||||||| |  ||||| ||||| |||||||| || || ||||||||||| |||||| || | || || ||| | | |||||| |
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatc-ttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 6

--tagtaacacttgg-tgtgttttcctcctgctgcatataactct-taatgcatttaagtttctgtttttttgtctgttcctgtaatccttgaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT
   ||||    | |  ||  || |        |   | |   |||  |    | | || |||||  ||| |||| |       |||||  | |   ||| | ||||||| || |  |||||||||||||||||||| || || |||||||| || || ||||| || ||||||||| |  ||||  ||||  |   |||||| |
acaagtagtcgtggaatgcattgtaggatcagtttctttctttctgcaggatagtaaaatttct--tttgttgtttaagatcttaatcagttat-attc-ttagATGACCAATAACATCCAGAAGAAGTTCAAGGTTTCTTCTACCCAACTCCTGTATCAGTCATGTCCTTATCAAGCCATGACATTGTTCATTGCTGGCCCAT

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 6

tagtaacacttggtgtgttttcctc-ctgctgcatataactcttaatgcatttaagtttctgt--ttttttgtctgttcctgtaatccttgaccgttcatc--agATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT
  |   || ||  |||||||   |  ||  | | | ||   | |   |  |||  |||    |  | ||| |||| |   |   ||| |   | |||| |   ||||||| || || |||||||||||||||||||| || || || |||||||| || || ||||| || |||||| ||||||| |||||  ||  |||||| |
aggctgcattta-tgtgtttcaataactatttcctctagggcct---gtctttgtgttgtaataatgtttagtct-tgtttaagatcttaatcagttccttttagATGACGAATACCATCCAGAAGAAGTTCAAGGTTTCTTCAACGCAACTGCTGTATCAATCTTGTCCCTATCAAGCACTGACGCTGTTCATCTCTGGCCCAT

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|32931475|gb|CF036287.1|CF036287

EST:     ACTCTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATT                         ATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTC
genomic: ACTCTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATTgtatcctttc ... cgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTC

EST: gi|32932218|gb|CF037030.1|CF037030

EST:     CGACTTGCATTGCTCAAATT                         ATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTC
genomic: CGACTTGCATTGCTCAAATTgtatcctttc ... cgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTC

EST: gi|76281072|gb|DV020640.1|DV020640

EST:     GATCCATACTCTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATT                         ATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCCACTGC
genomic: GATCCATACTCTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATTgtatcctttc ... cgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGC

EST: gi|71770743|gb|DR968680.1|DR968680

EST:     GATCCATACTCTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATT                         ATGACAAACACTATCCAGAAGAAGTTCA-GGTCTCATCGACCCAACTGCTC
genomic: GATCCATACTCTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATTgtatcctttc ... cgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTC

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: 170

TCTTGGTGTTGGTGTTGCAACTGTCACTGATCTGCAACTCAATGCTGTGGGATCCATACTCTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATTgtatcctttc ... cgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT

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

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 177

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 291

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttaagtttctgtttttttgtctgttcctgtaatccttgaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT

                                    atccttgac  putative branch site 
              tgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtaacacttggtgtgttttcctcctgctgcatataactcttaatgcatttaagtttctgtttttttgtctgttcctgtaatccttgaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT

- - - - - - -tgtgttt
- - - - - - - - - - - - cctgctg
- - - - - - - - - - - - - - - - - - - - - - atgcatt