ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGCTACTAGCATGCATTTGGATAATGATGTGGAGGACCTAGAGATGTTACTTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctctttatccacactgaaacataatgtattctcctgtattgtgggttctgtaattatatggtgctgtctcatgagacataaacataatctgctt...

Basic information

species	Zea mays
transcript	GRMZM2G145794_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G145794_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g39790.4 (Oryza sativa), 5'ss of exon 2

TGCTACTAGCATGCATTTGGATAATGATGTGGAGGACCTAGAGATGTTACTTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctctttatccacactgaaacataatgtattctcctgtattgtgggttctgtaat--tatatggtgctgtctcatgag-acataaacataatctgctt
 ||||| |||||||||||||||||||| ||||| |||||||| ||||| |||||||| |||||||||||  ||||||||||||||||||||||||||||||||||||  |||| ||| | |||||     |   | |   | || |  |   |   ||||  ||||||       ||  ||   |  |  || || |||    
CGCTACAAGCATGCATTTGGATAATGACGTGGAAGACCTAGAAATGTTGCTTGAGGCTTACTTCATGCAATTGGATGGAATTCGCAACAGAATTTTGTCGgttagtccttttacccatattgaaatggggtagttgcagttttacttggatctacttaatgctatatgacttatcctagtgttcatttggacttattctc---

upper sequence: GRMZM2G145794_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G13340.2 (Glycine max), 5'ss of exon 3

-TGCTACTAGCATGCATTTGGATAATGATGTGGAGGACCTAGAGATGTTACTTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctctttat-ccacact---gaaacataatgtattctcctgtattgtgggttctgtaattatatggtgctgtctcatgagacataaacata-atctgctt
   |  | |  |||    || ||||  ||||||||||| | |||||||| ||||| || || ||||||||| ||||||||| ||| |||| ||| || || ||  || |  | |  ||| | |   |  | ||||||| | ||     ||| ||     || || | |       | |||  |  ||    | | |  ||||  ||
GACCAGCCATTATGAGGATG-ATAACAATGTGGAGGACTTGGAGATGTTGCTTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCAgtatgtattctaacaccatattctggtcaaataatgtgt-ctgtcaaattttgaagattgaaactgt----cattttctatttggattctatcgtctatctaatt

upper sequence: GRMZM2G145794_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G30180.1 (Glycine max), 5'ss of exon 3

-TGCTACTAGCATGCATTTGGATAATGATGTGGAGGACCTAGAGATGTTACTTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctctttat--ccacact---gaaacataatgtattctcctgtattgtgggttctgtaattatatggtgctgtctcatgagacataaacata-atctgctt
   || | |  |||    || ||||  ||||||||||| | |||||||| ||||| || || ||||||||| ||||||||| ||| |||| ||| || || || ||| |  | |   ||| |||   |  | || |||| | ||     ||| ||     || || | |     | | |||  |  ||    | |||  ||||  | 
GACCTGCCATTATGAGGATG-ATAACAATGTGGAGGACTTGGAGATGTTGCTTGATGCATATTTCATGCAGTTGGATGGAACTCGTAACAAAATATTATCTgtaagtattctaacaaccatactctggtcaaatcatgtgt-ctgtcaaattttgaaggatgaaactgt----cgttttctacttggattctatcatctatctaat-

upper sequence: GRMZM2G145794_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv12s0034g02550.t01 (Vitis vinifera), 5'ss of exon 3

TGCTACTAGCATGCATTTGGATAATGATG---TGGAGGACCTAGAGATGTTACTTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctctttatccac-actgaaacataatgtattctcctgtattgtgggttctgtaattatatggtgctgtctcatgagacataaacataatctgctt
    |||||||    | ||||| ||||||   ||||||| || |||||||| |||||||| ||||||||||||||||| || | ||| ||||  || ||||| || ||| |    ||     | |  |    |   || |      || ||  |    |  ||  ||||  ||||   |  ||   ||   |  |  |    ||
---AACTAGCAACTTTGTGGATGATGATGATGTGGAGGATCTGGAGATGTTGCTTGAGGCATACTTCATGCAGCTGGACGGGACTCGTAACAAGATATTGTCTgtaagtattaccattattgattatagttgagcctagttaaagttactgatgaagata-aaccatattttgcttcatgttgctccactgagttccttaaatt

upper sequence: GRMZM2G145794_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S56_118V6.1 (Physcomitrella patens), 5'ss of exon 2

TGCTAC-TAGCATGCATTTGGATAATGATGTGGAGGACCTAGAGATGTTACTTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctcttta-tccacactgaaacataatgtattctcctgtattgtgggttctgtaattatatggtgctgtctca---tgagacataaacataatctgctt
   ||| ||||  |      |   |||| || ||||| || ||||||||||| |||||||||||||||||| | ||||     |  ||||   | | |  ||| ||| |||  | |||   |    | ||||  | |  ||    | | ||| |      | |  | |     |  ||    |||  |  |   | || |     
-TTTACATAGCTCGGGCAGAGTCTATGAAGTTGAGGAGCTGGAGATGTTACTAGAGGCCTACTTCATGCAGGTTGATGCTGGCCTTAACAAGCTCTCGCTGgtgagtttctaaaatccgagcaatcagataacttgtattcaaacagtctggatgtccagagttcaagtcatcgattctatctgattcccattgagaaacc----

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|44682071|gb|CK787119.1|CK787119

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|211090936|gb|FL430965.1|FL430965

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|211090937|gb|FL430966.1|FL430966

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGAGTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|86469276|gb|DY235646.1|DY235646

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|89759049|gb|DY687995.1|DY687995

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATG
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATG

EST: gi|149086561|gb|EE176104.2|EE176104

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|71760155|gb|DR958092.1|DR958092

EST:     TGAGGGCNTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TGA-GGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|76292915|gb|DV032483.1|DV032483

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|88747345|gb|DY531486.1|DY531486

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|33468182|gb|CF245231.1|CF245231

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|211093386|gb|FL430967.1|FL430967

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATCCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|60351854|gb|DN218827.1|DN218827

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|76016576|gb|DT943746.1|DT943746

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|71759716|gb|DR957653.1|DR957653

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|91055353|gb|EB165771.1|EB165771

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|71758746|gb|DR956683.1|DR956683

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|211210677|gb|FL438027.1|FL438027

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

EST: gi|93016531|gb|EB642051.1|EB642051

EST:     TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCG                         GTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC
genomic: TTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGAC

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: 44 (upstream exon), 37 (downstream exon)
Score: 16

TGCTACTAGCATGCATTTGGATAATGATGTGGAGGACCTAGAGATGTTACTTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctct ... aataaaacagGTTCGGGAGTATATTGATGACACAGAAGACTACGTCAACATTCAACTCGACAACCAGCGTAACGAACTCATTCAACTCCAGCTTACACTTACGATTGCAT

Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 22

Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 32

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 41

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTACTAGCATGCATTTGGATAATGATGTGGAGGACCTAGAGATGTTACTTGAGGCCTACTTCATGCAGCTGGATGGAATTCGCAACAGAATTTTGTCGgttagtctctttatccacactgaaacataatgtattctcctgtattgtgggttctgtaattatatggtgctgtctcatgagacataaacataatctgctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA