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

gcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG

Basic information

species	Zea mays
transcript	GRMZM2G086486_T02
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g42380.1 (Oryza sativa), 3'ss of exon 4

gcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
||||| ||| ||    |  ||| |   | ||    |  || || |        | ||| |||||   || | | | ||| ||| || |  || ||||| |||||||| |||||||| || ||||| ||||||||||| ||||| ||||| |||||||||||||| ||||||||||||||||||||
gcaagttaacctg-gttgctgggtatcagttctataatgcctcat-----tgggctgtttgttcataaaatta-attttattgatgctgatgcagGTACGAGAAGAGGCACTCCAATATTCCTGCTCACATTTCACCGTGCTTCCGTGTTAAGGAAGGAGATCACGTGATCATTGGCCAGTGCAG

upper sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G12430.1 (Glycine max), 3'ss of exon 4

gcaagctaatcttcaata---ttggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
      |   |||| |||   ||||   | | ||| || |   | | ||     | ||      |        |  |  |||| |  | | | | ||| ||||| ||| | || || || || ||| | ||||| ||||| || || ||||| ||||||||||||||||| || |||||||| |||||
--gtattccccttccatacctttggtgagcagttattgttgtttacatggacagaagtaactaat------gtttcttctttgctcat-tctatttagATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG

upper sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G11430.1 (Glycine max), 3'ss of exon 4

gcaagctaatcttcaata-ttggcttgtatttactgatcgcttcgtgccttcatgt-tgtctgttcg--ccaactgataatt---tgttggtgtttgtgt--agGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
      || ||| |   | |    |||| || | |  | | || ||  | |  ||| ||| ||      |  | | ||||||   | ||  | ||| ||   ||||| ||||| || ||||||||||| ||||| || || |||||    || ||||| |||||||||||||| || || ||||| || |||||
--gtattattctcctgcaatccttttgtgttcatt--ttgttttgtttcgttttgtatgtttggagaaacataattataattccattttcatttttatgctcagGTACGAGAAAAGGCACTCCAACATTCCTGCTCATATATCACCTGCTTTCCGTGTGAAGGAAGGAGATCACGTTATTATTGGTCAATGCAG

upper sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT3G48930.1 (Arabidopsis thaliana), 3'ss of exon 4

gcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
      |||  |   | |||  ||  || ||  |  ||  |     | | ||  |||    ||    || | |||   | || ||  |    ||||||||||||||| || || ||||| || || ||  | ||||||||||| ||||| ||||||||||| ||| | ||||||||||| |||||
-----gtaaattcatacatt--ctcatacttctt--tccatagagtcttacacattgatgtttaagaaagtaatatcctttttgttct----tagGTATGAGAAGAGGCATTCAAACATTCCGGCTCATGTCTCACCATGCTTCCGTGTTAAGGAAGGAGACCATATCATCATTGGCCAATGCAG

upper sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT5G23740.1 (Arabidopsis thaliana), 3'ss of exon 4

gcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtg--tagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
| |||   ||  |    ||   | | | ||   |||| |    | ||    || |    |    ||  |   |  |||   |    ||| |   ||| |||||||||||||| |||||||||||||| ||  | ||||| || || |||||||||||||| || ||||| ||||||||||| |||||
gtaagtacattgtg---atgaacctatgttc-ttgatagagctgcgcaaagatataacatcaatgctgataaacgattatcttaaatttttcattagATATGAGAAGAGACATTCCAACATCCCTGCCCATGTCTCACCGTGTTTCCGTGTCAAGGAAGGTGACCATGTCATCATTGGCCAATGCAG

upper sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 3'ss of exon 4

gcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
| | |      || ||| |       | |||  |  |||    |  ||||  | |||| ||      || |  ||| ||||   |||   | ||| ||||||||||| ||||| || || || || || || || |||||||| |||||||| || || |||||||| || ||||||||||||||
gtaggaaccgatttaat-tgaatgaatctttgtttttcgg---gctcctttctcttgtatggaatataa-tattaaattgt-attgtcactctagATATGAGAAGAGGCACTCAAATATACCAGCACATATATCCCCATGCTTCCGTGTCAAAGAGGGTGATCATGTTATTATTGGCCAGTGCAG

upper sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4

gcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttg-----tgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
||| | |   || || |  | | |   | |   |  |       | ||   |  |||  | |     |  |||  |||| ||  | ||||     |  || ||||||||||| ||||| ||||| ||||| ||||  || |||||||| ||||| ||||||||||||||||| || ||||||||||||||
gcatgtt--cctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG

upper sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ16024 (Selaginella moellendorffii), 3'ss of exon 4

--gcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
  |   | ||  |   | |  |  |  || | | ||     | ||| |  |   |   |  | |   ||||   | ||||  ||  | ||| |  |||||||| ||||| ||||| ||| |  | || ||  | || || |||||||||||||||||||||||| | |||||| | |||||||||||
gtgagtgttaggcccaagttcttccaagtttcttctttcgtcctcgcgattctctcgcgattctcatccaa---aaaattcttt--tttttattcagGTATGAAAAGAGGCACTCAAACGTGGCAGCTCATGTGTCGCCGTGCTTTCGTGTCAAGGAAGGAGATAAAGTGATCCTCGGCCAGTGCAG

upper sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ07974 (Selaginella moellendorffii), 3'ss of exon 4

gcaagc-taatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
|  ||  |   |   | |  |  |  || | | ||  |||| ||| |  |   |   |  | |   |||    | ||| | ||    ||| |  |||||||| ||||| ||||| ||| |  | || ||  | || || |||||||||||||||||||||||  | |||||| | |||||||||||
gtgagtgttggcccaagttcttccaagtttcttctt-tcgcctcgcgattctctcgcgattctcatccag--aaaaatctctt----ttttttcagGTATGAAAAGAGGCACTCAAACGTGGCAGCTCATGTGTCGCCGTGCTTTCGTGTCAAGGAAGGAGACAAAGTGATCCTCGGCCAGTGCAG

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|211165025|gb|FL430212.1|FL430212

EST:     ACCATCATTGTTCGTAGGAATTATCTTCACTTCGTCAAGAAGTACCAGAG                         GTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTCCG
genomic: ACCATCATTGTTCGTAGGAATTATCTTCACTTTGTCAAGAAGTACCAGAGgcaagctaat ... gtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG

EST: gi|211069694|gb|FL093950.1|FL093950

EST:     ACCATCATTGTTCGTAGGAATTATCTTCACTTCGTCAAGAAGTACCAGAG                         GTATGAGAAGAGACACTCCAACATCCCTGCGCACA
genomic: ACCATCATTGTTCGTAGGAATTATCTTCACTTTGTCAAGAAGTACCAGAGgcaagctaat ... gtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACA

EST: gi|211378928|gb|FL475785.1|FL475785

EST:     ACCATCATTGTTCGTAGGAATTATCTTCACTTCGTCAAGAAGTACCAGAG                         GTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTCCG
genomic: ACCATCATTGTTCGTAGGAATTATCTTCACTTTGTCAAGAAGTACCAGAGgcaagctaat ... gtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG

EST: gi|211069693|gb|FL093949.1|FL093949

EST:     ACCATCATTGTTCGTAGGAATTATCTTCACTTCGTCAAGAAGTACCAGAG                         GTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG
genomic: ACCATCATTGTTCGTAGGAATTATCTTCACTTTGTCAAGAAGTACCAGAGgcaagctaat ... gtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG

EST: gi|211069690|gb|FL093946.1|FL093946

EST:     ACCATCATTGTTCGTAGGAATTATCTTCACTTCGTCAAGAAGTACCAGAG                         GTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG
genomic: ACCATCATTGTTCGTAGGAATTATCTTCACTTTGTCAAGAAGTACCAGAGgcaagctaat ... gtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG

EST: gi|84980019|gb|DW530368.1|DW530368

EST:     ACCATCATTGTTCGTAGGAATTATTTTCACTTCGTCAAGAAGTACCAGAG                         GTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG
genomic: ACCATCATTGTTCGTAGGAATTATCTTCACTTTGTCAAGAAGTACCAGAGgcaagctaat ... gtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG

EST: gi|211069688|gb|FL093944.1|FL093944

EST:     ACCATCATTGTTCGTAGGAATTATCTTCACTTCGTCAAGAAGTACCAGAG                         GTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG
genomic: ACCATCATTGTTCGTAGGAATTATCTTCACTTTGTCAAGAAGTACCAGAGgcaagctaat ... gtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCG

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: 111

TCAGGGGTCGCATCATCGCTGGAACATGCCACAGTGCTAAGATGAATAGGACCATCATTGTTCGTAGGAATTATCTTCACTTTGTCAAGAAGTACCAGAGgcaagctaat ... gtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG

Block sizes: 43 (upstream exon), 44 (downstream exon)
Score: 39

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 74

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 64

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG

                           aactgat  putative branch site (score: 64)
                                ataatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA