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

...tcgctttgagcggatgtgtttgacatggtgaattgggtgtatttctgccgacatatttgcttgttctcttctgaacttgtccccctttatttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA

Basic information

species	Zea mays
transcript	GRMZM2G011101_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g17430.1 (Oryza sativa), 3'ss of exon 3

tcgctttgagcggatgtgtttgaca-tggtgaattgggtgtatttctgcc-gacatatt--tgcttgttctcttctgaacttgtccccctttatttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA
     ||   | |||   |   | | || ||    |    |    || |  | ||||||  |  | |   |  ||     |      | |  |  | || |||||||||| || ||||||||||| ||||| || || ||||| ||||||||||||||||| || ||||| ||||||||||| || |||||||| |||||||| 
----gttagccagataactggaaaactgttgtcccgtacattccactacttgtcatattaataatagggttaatcactcttctaattcataaaccttatgccagGTCTGCGCTTGACGGAGAATGCGGTTTTCTCGCCGCTAACCTTTATGCAAAGAGTGTTTTCGGTGAAGATGCTTTGGTAAATATCAGCATCGAGAAGCAG

upper sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3

-----tcgctttgagcggatgtgtttgacatggtgaattgg-gtgtatttctgccgacatatttgcttgttctcttctgaacttgtccccctttatttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA
     |     | |  |  ||    | | |   ||   ||   ||  ||| ||  |||  |||  | | |  || | ||    | | |    || |||| |   || || ||| | || || || ||||| ||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||  | |||||||| ||||||
cgtactaatcattaatgtgtggacataaaacattgttatgtcatgattttatggggacccattc-catataatcatttgg---tttgcgttgttgtttgtt--tagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA

upper sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G00610.1 (Glycine max), 3'ss of exon 3

tcgctttgagcggatgtgtttgacatggtgaattgggtgtatttctgccgacatatttgcttgttctcttctgaacttgtccccctttatttgatacc-----agGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA
    | | |    |    ||| |  |     | |     |   | |   ||||||     ||||| | |  |||  || |     |||  ||| |        || || ||| | || || || ||||| ||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||  | |||||||| ||||||
----tattatttca-acatttcatgttacttactaatcattaatgtatggacataaaacattgttatatcttgattttatggggttttggttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA

upper sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G31490.1 (Arabidopsis thaliana), 3'ss of exon 4

tcgctttgagcggatgtgtttgacatggtgaattgggtgtat-ttctgccgacatatttgcttgttctcttctgaacttgtccccctttatttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA
                     |  |  || ||||     |   | |||  || |        |    ||||   || |  | |  ||||| |||    ||| |||||| |||  || |||||||| |||||||| || ||  | |||||||| ||||||||||||||||||||| | |||||  | || ||||||||||||
---------------------gtaagtgtaaattcttctttcatcctgtagaaacgaaaaact--cgtcttactaattaatacttctttacttg----cagATCTGCAATAGCAGGTGAATGTGGATTCCTTGCAGCAAACTTATATGCAAAAAGTGTGTTTGGTGAGGATGCTCTTGTGAATTTGAGTATTGAGAAGCAA

upper sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 3

---tcgctttgagcggatgtgtttgacatggtgaattgggtgtatttctgccgacatatttgcttgttctcttctgaacttgtccccctttatttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA
     |   |  | |           ||  |    ||   ||| || |     ||| |     |  || |    |   |||||   |  |  || | |  |||||| ||||| || || || ||||| ||| | |||||||| || ||||||||||| |||||||| |||||||| ||||| ||||| ||||||||||| || 
ggggtgaaattcgtgtccaaacacatcactgcttcttccttgtcttacctaataca-acccattcatttttcattctccttgttggc--tggttgggtttcagGTCAGCACTGGATGGTGATTGTGGATTCTTGGCTGCTAACCTCTATGCAAAGAGCGTGTTTGGGGAGGATGCCTTGGTAAACATAAGCATTGAGAAACAG

upper sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S309_15V6.2 (Physcomitrella patens), 3'ss of exon 4

tcgctttgagcggatgtgtttgacatggtgaattgggtgtatttctgccgacatatttgcttgttctcttctgaacttgtcccccttt---atttgatac---cagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA
    | | |   |||  | ||   ||| |   ||   |  |  | |  | |||  |||   ||   |  || ||  ||||  | |  |   || |  |||   ||| |||||  | || || || ||||| ||  | || || ||||||||||| ||||| |||||||| |||||||| ||||||||  ||||  |||||||||||
----tgtaacgtgata-gcttttgatgattttttcaatcaaacttttgccaca-gtttaagtgaaatgatccgagtttgtaacacacttgaatcttgtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAAGAGCGTGTTTGGAGAGGATGCGTTGGTGAATGTCAGTGTTGAGAAGCAA

upper sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S42_100V6.1 (Physcomitrella patens), 3'ss of exon 4

----------------------------------------tcgctttgagcggatgtgtt-tgacatggtg----aattgggtgtatttctgccgacatatttgcttgttctcttctgaacttgtccccctttat--ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA
                                        |  ||||  ||   | | |  | | ||  ||    ||| |    | | || |  ||| || ||  ||    |  ||| |  ||   |    || |  |    | |||||||||| | || ||||| |||||||| |||||||||||||||||||| |||||||| ||||| |||||||||||||| ||  | ||||||||||| |||
gtaagtctttgtttacacctgcaagtaatatctggtcttttatcttttcgcctttttttcataatatcatgttataatggaagatgtatcgggtgacctacttcattccgttaatctaatttttcgctttattgtcgtcatgagcagGTCTGCATTGGAGGGAGACTGTGGTTTTCTTGCTGCTAATCTTTATGCTAAGAGTGTTTTTGGAGAGGATGCTTTGGTCAATGTTAGCATTGAGAAACAA

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|74236156|gb|DT644070.1|DT644070

EST:     TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|78179458|gb|DV549831.1|DV549831

EST:     TTCTTGAATCACATTATCAAATCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|211489682|gb|FL122965.1|FL122965

EST:     TTCTTGAATCACATTATCAAATCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|84976649|gb|DW475071.1|DW475071

EST:     TTCTTGAATCACATTATCAAATCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|33093348|gb|CF053342.1|CF053342

EST:     TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|32929197|gb|CF034009.1|CF034009

EST:     TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|24934221|gb|CA452439.1|CA452439

EST:     TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|149076797|gb|EE165446.2|EE165446

EST:     TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|60341135|gb|DN208108.1|DN208108

EST:     TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|6827494|gb|AW331137.1|AW331137

EST:     TTCTTGAATCACATTATCAAATCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|33094919|gb|CF054913.1|CF054913

EST:     TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

EST: gi|32790600|gb|CD942836.1|CD942836

EST:     TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC                         GTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA
genomic: TTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 286

GTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACCgtaagttgtt ... ttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 197

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 284

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgccgacatatttgcttgttctcttctgaacttgtccccctttatttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA

                                           atttgat  putative branch site (score: 284)
                              cttgtccccctttatt  CT-rich tract
                                        tttatttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgctttgagcggatgtgtttgacatggtgaattgggtgtatttctgccgacatatttgcttgttctcttctgaacttgtccccctttatttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - tgtgttt
- - - - - - - - - - - -catggtg
- - - - - - - - - - - - - - - - - - - - - ttctgcc