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

...gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

Basic information

species	Zea mays
transcript	GRMZM2G152127_T01
intron #	15
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15

gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgtt--cactgccaaatattaatat-ttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
 | || | |   |    || |  || ||  | ||||| ||| ||   | ||  |||   |  || | || ||   || | |  |  || |||| |||||| ||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||| || ||||| || || || || |||||
-ttttcatatcaaaagagact-gacctgttaacagaa-tgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15

gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
||  |   |   ||  |     || |||   |    | |  |||  |     |     |||  |  |||  |   |   ||  | | |||| | |  |||| || ||||| ||||||||  || ||||||||||||| || ||||| || |||||||| || || ||||| ||||| ||||| || ||||| || || ||
gttatttcatttatgttttccaaatttgaggtttatatt--cttatattagctgttgggtcacagttttcctttttattaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15

----gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
     ||||       |     ||  || | |  |  | |   |  |||| | |      |  |||      |  ||||   |   |  | ||| |     |||| ||  |||||||||||||  | || |||||||||||||| |||||| | |||||||| ||||| || |||||||| |||||||| |||||||| |||||
gtatttctttctctgaacttgtatacaattagttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactc---tcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15

---------gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
           | | ||     |  | ||||  ||| ||   | | | || ||| |||| |       | |     || || | |   || |||   ||| |    |||| ||  |||||||||||||  |  | |||||||||||||| |||||||| || |||||||||||||| ||| | || |||||||| || || ||||||||
gttactaaaaacctcaacactttgatcattttgctttcctatatata-gcattttaaatatcagttcttatttaccttatttaat-ttaactatgtgtatcttac-cagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15

----gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcac--tgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
    |     |  |  ||      || | ||    |  ||  | |  |    |||||    | ||     |||    ||  |||  |  | | || |||    |||| ||  |||||||||||||  |||| || |||||||| || || ||||||||||||||||| |||||||| ||||| ||||| |||||||| ||||||||
gtttgctcatattggcatttcttcttgaattaagttttgaggtcctct----attttgtggattcgtttctttaacaaccttgctgatgacttatcttt-tcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
lower sequence: EDO96800 (Chlamydomonas reinhardtii), 3'ss of exon 12

--------------gtcttgaaagagatcctgattta-acttgccatcagaaatgcctttgaa-------attttcccaagtcta-acgtttgttcactgccaaatattaatatttac-tgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
                 || | | | |  |  |   | ||   |   || | |  |    | |       |    | |||    | ||||     ||| | |    |    |  || |   | || ||| | || |||  |  | | ||||||| | | |||||||| |||||||||||||||||||||||||||   ||                        
tgttttccttgtgctctttaacacacacacacacacacacacacacacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA------------------------

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
lower sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16

----------------------------------------------------gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatattt-----actgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
                                                     | ||     |||   ||  ||    |  | |  ||| ||  | |   |           ||   |  | |   || |    |  |  | ||      |||||||| || || || |||||| ||   || |||  | |||||||||| ||| | |||||||||||||||||| | |||||||| || |||||||| || |||||
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15

gtcttgaaagagatcctgatttaacttgccatcagaaat-gcctttgaaattttcccaagtctaacgtttgttcactgccaaatatt----aatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
     |     | || |||  ||  |||  |  |  |     |||||      |    |    || | |    ||  | ||| |  |     || | |    |||| || ||||| ||||||||    || ||     ||||||| ||||| ||||||||||||||||||||||| || || ||||| |||||||| || || ||
---caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtcaatgatga--catagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA

upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15

-------gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
        | |     || |    |||  |  ||      |  ||||    || |        |   || | || |  | | |     |||   ||   |    |||| || ||||| ||||||||| | || || ||||||||||| |||||||| |||||||| || |||||||| || |||||||| ||  |||| || || ||
gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggag----agcgctgatgtattctgattcttttata---atgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA

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|71768490|gb|DR966427.1|DR966427

EST:     GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAG                         GAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA
genomic: GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAGgtaccatcgg ... tttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA

EST: gi|33096859|gb|CF056819.1|CF056819

EST:     GAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAG                         GAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA
genomic: GAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAGgtaccatcgg ... tttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA

EST: gi|86470254|gb|DY236624.1|DY236624

EST:     GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAG                         GAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA
genomic: GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAGgtaccatcgg ... tttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA

EST: gi|33770959|gb|CF273253.1|CF273253

EST:     GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAG                         GAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA
genomic: GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAGgtaccatcgg ... tttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA

EST: gi|74246154|gb|DT654068.1|DT654068

EST:     GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAG                         GAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA
genomic: GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAGgtaccatcgg ... tttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA

EST: gi|74239652|gb|DT647566.1|DT647566

EST:     TCTTGGTCGATGGCTGGTTCCACACAG                         GAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA
genomic: TCTTGGTCGATGGCTGGTTCCACACAGgtaccatcgg ... tttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA

EST: gi|211444856|gb|FL116921.1|FL116921

EST:     GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAG                         GAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA
genomic: GCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAGgtaccatcgg ... tttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCA

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: 222

CGTGGGGAAATTTGCATCAGAGGGGACACCTTGTTCTCGGGATACTACAAGCGAGAGGACCTAACCAAAGAAGTCTTGGTCGATGGCTGGTTCCACACAGgtaccatcgg ... tttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

                                     tattaat  putative branch site (score: 286)
                                  aaatattaatatttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - -gatcctg
- - - - - - - - - - - - - -gccatca
- - - - - - - - - - - - - - - - - - - tgccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgcca