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

...atgtgacctcccacagtcccacccctcctacacctttcacgatagcctaatgggtcatattatcactatgttttatttgatttcctcttcttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT

Basic information

species	Zea mays
transcript	GRMZM5G823629_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G823629_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 4

atgtgacctcccacagtcccacccctcctacacctttcacgatagcctaatgggtcatattatcactatgttttatttgatttcct--cttcttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT
 | || |  |  | ||          |||   |    |||  |  | |      |  | ||| ||||||   || |||  |||| |  ||||| | || ||||||||||| || |||||| ||||||||||||||||||||||||| ||||| || |||||||||||||| ||||||||||| ||  || || |||||||||
gtttgtctgctaatagaagtcttgtcccttttctacgcacttt--catggcaaattttcttaacactattacttgttttgtttctttgcttctgtgctgcagTATGTTCATCACCTTCAAAGGAAGTACTCGCTTGGCTCATTCAACCTCTTGGGTCATACTGCTCCAGCTCAGGCAGCATCTTTACTAGTACTGGGGCCTT

upper sequence: GRMZM5G823629_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4

-atgtgacctcccacagtcccacccctcctacacctttcacgatagcctaatgggtcatattatcactatgttttatttgatttcctcttctttt---ctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT
 |    |  |    |  || |  |  |  | ||| ||| | | |    |  ||| | ||  || |||| |||||||||  | ||  | ||||||    || ||||| ||||| || ||||||  |||||||||||||||||||||||| || || || |||||||||||||| |||||||||||  |||||||| |||||||||
aacagaaattttgtccctcgctgctgtttt-cacttttaatggtgaggttttggataat--tagcact-tgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT

upper sequence: GRMZM5G823629_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4

atgtgacctcccacagtcccacccctcctacacctttcacgatagcctaatgggtcatattatcactatgttttatttgat-ttcctcttcttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT
                            ||     ||   | ||   |        | ||||  | || | ||||    |  || ||||  |||  | |||||||| ||  |||| ||  | |||||||||||| |||||||||| ||  | || |||||||||||||| ||||| ||| | || || ||||| || || |
---------------------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT

upper sequence: GRMZM5G823629_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 4

--atgtgacctcccacagtcccacccctcctacacc-tttcacgatagcctaatgggtcatattatcactatgttttatttgatttcctcttcttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT
  ||    |   |   |||   |    |     ||  | | |  |     |||  |   |  || | ||  ||  | | ||   || ||  |  | ||| |||||||| ||   ||||||| ||||||| ||  | ||||||||||| || || || ||||||||||||| |||||| |||||  || |  || | || || |
ccatacccctgtcactagtttaagttatagattactatctgattaacatgtaaatgacta-gttttgac--tgactcaattctgttactgattatgtctgcagTATGTGCATTTTCTTCAACGGAAGTATTCCTTAGGCTCATTCAACCTATTGGGGCATACTGCTCCAGTGCAGGCTGCATCTCTGCTGTTATTAGGACCCT

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|78079408|gb|DV507820.1|DV507820

EST:     GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACAT                         TATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA

EST: gi|76280570|gb|DV020138.1|DV020138

EST:     GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACAT                         TATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTNCA-TCTCTT
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATT-CAATCTCTT

EST: gi|71445237|gb|DR826287.1|DR826287

EST:     GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACAT                         TATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA

EST: gi|76281274|gb|DV020842.1|DV020842

EST:     GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACAT                         TATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTNCA-TCTCTT
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATT-CAATCTCTT

EST: gi|78111635|gb|DV530032.1|DV530032

EST:     GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACAT                         TATGTTCACCATC
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATC

EST: gi|60337491|gb|DN204464.1|DN204464

EST:     GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACAT                         TATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA

EST: gi|67012439|gb|CO441188.1|CO441188

EST:     GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACAT                         TATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA

EST: gi|31364467|gb|CD448822.1|CD448822

EST:     GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACAT                         TATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA

EST: gi|37401537|gb|CF638135.1|CF638135

EST:     GGCTATTAGCTGCAGTAATAGCTGTTT-GAGCACAGCACTACAACAACAT                         TATGTTCACCACCTTCAATGGAAGTACTCGC-TGGCTCNATTCAATCTCTT
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTC-ATTCAATCTCTT

EST: gi|76015509|gb|DT942679.1|DT942679

EST:     GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACAT                         TATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA
genomic: GGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTA

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), 46 (downstream exon)
Score: 73

CATAGGTGTTGCTGTGTGTACTGTGACTGATGTTAGCGTGAACTCTCAAGGGCTATTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAACAACATgtgagtattg ... ttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 117

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 89

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 84

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cctaatgggtcatattatcactatgttttatttgatttcctcttcttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT

                       tgttttatttgatttc  CT-rich tract
           atattatcactatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgacctcccacagtcccacccctcctacacctttcacgatagcctaatgggtcatattatcactatgttttatttgatttcctcttcttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT

- - - -ctcccac
- - - - - - - - - ccacccc
- - - - - - - - - - - - - -ctacacc