ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcactcttatcacttatatacgcagtttctcacctaggagatgttggatgtggttttcttactctacaaaggagaaggacaacaactttt...

Basic information

species	Zea mays
transcript	GRMZM2G006672_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 5'ss of exon 2

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcactcttatcacttatatacgcagtttctcacctaggagatgttggatgtg--gttttcttactctacaaaggag-aaggacaacaactttt---
|||||||||||  ||||| ||||||||| |||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| |||| ||   ||| |||| |  ||| |      ||| | | |    ||  ||  |||   ||   | || |||| |       |  ||      |||||   
TGAGGTTGCAACAAAGTATCCTGGAATTCAATATAATGAAATCATCGTGGACAACTGTTGTATGCAGCTTGTTGCTAAGCCTGAACAATTTGATGTTATGgtaagtatgttagttct-atcattactatgca-----tcttaacaaatgcattctgtttgtaacgtcaccatattctatactcacctactgatctatgcttttatc

upper sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G08920.1 (Glycine max), 5'ss of exon 2

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcactcttatcacttatatacgcagtttctcacctaggagatgttggatgtggttttcttactctacaaaggagaaggacaacaactttt--------
 |||||||| |  | ||| |||||||| || || |||||||| ||||| |||||||| || |||||||||||| |||| || || || |||||||| |||||| ||| ||| ||| || | |     || | || ||  | | ||        || ||| |  |    | |   |  ||    |  |||  |   ||| |        
AGAGGTTGCCACAAGGTATCCTGGAATCAAGTACAATGAAATTATTGTAGACAACTGCTGCATGCAGCTTGTTTCAAAACCGGAGCAGTTTGATGTCATGgtatgtaaatttactatt-tgatcctgattctcaattatttatctgc------tttgat-taatacattcatggtgtaattatgggggatcaatgcttgtttgcttcc

upper sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G22640.1 (Glycine max), 5'ss of exon 2

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcactcttatcacttatatac-gcagtttct-cacctaggagatgttggatgtggttttcttactctacaaaggagaaggacaacaactttt
 |||||||| |  |||||||||||||| || ||||| ||||| |||||||| ||||| ||||||||||||||| ||||||||||||| |||||||| |||||| || |||| ||  |     ||  | | | || |||| | ||| || |  || |||  | |  | |  |||  |   ||      |   |    | ||  
AGAGGTTGCTACAAAGTACCCTGGAATAAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacattctattctggtttgctgctgtttatgcacttatgtaattttg--tctaatgtatttatgcagtaagcacacacacccttgagttaa

upper sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcac-tcttatcacttatatac-gcagtttct-cacctaggagatgttggatgtggttttcttactctacaaaggagaaggacaacaactttt
 |||||||| |  |||||||||||||| || ||||| ||||| |||||||| ||||| ||||||||||||||| ||||||||||||| |||||||| |||||| || |||| || | | |   ||    | | ||  ||| | ||| || |  || |    | |  | |  ||   |   ||       |  |  |  |    
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttgcagctatttatgcacttatgtaattt---gtctaatgtatttgtgcagtaacccccccgccccccgcccccc

upper sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 2

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcactcttatcacttatatacgcagtttctcacctaggagatgttggatgtggttttcttactctacaaaggagaaggacaacaactttt---------
 |||||||| || ||||| ||  | || |  || |||||||||||||| || ||||| |||||||| ||||| || || || || ||||| ||||| |||||| ||   ||||   ||||     ||| |      || |||   | |   | |  |   | | | | ||||| |   ||  |||       || || |          
CGAGGTTGCGAAAAAGTATCCCAGCATCACCTACAATGAAATCATTGTTGATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgt---ttcagagttat-----atacatatgaattttcatg-acgttctttaagtcttcgatgttttactttgagaaaaagataccagtcatctctccctagtttg

upper sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 5'ss of exon 2

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgta-----cgtatattcactcttatcacttatat--acgcagtttctcacctaggagatgttggatgtggttttcttactctacaaaggagaaggacaacaactttt----------------
 |||||||| ||  | ||  | || ||||  || |||||||| || || ||||| || |||||||||||||| || |||||||| ||||||||||| ||||||     | | | |||    |||  | | | |   |  || |||   |  |   ||| | || |       ||  |  | |    | |      |     | ||||                
AGAGGTTGCTAAACATTATTCGGGGATTACTTACAATGAAATAATCGTAGACAATTGCTGTATGCAGCTTGTCGCCAAGCCTGAGCAATTTGATGTCATGgtaatgctcttcttttcctagttacaaatcaaaatgagtcattttgaaatgtgacagacgatgaaaccatcattgatgttgttttgatgtctctcatggatattttttgttggtttgtttcag

upper sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 2

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcactctt--atcacttatatacgcagtttctcacctaggagatgttggatgtggttttcttactctacaaaggagaaggacaacaactttt
 || ||||| || || |||||  | |||  ||| |  ||||| |||||||| ||||| || ||||| || ||| ||||||| || ||||||||||| |||||| ||   ||  |   |  ||   ||  ||  | |   | ||   |||    |  |     || | || |||||  | | | |       | | ||  |  
GGAAGTTGCGAAAAATTACCCCAGTATTGCATACAGCGAAATTATTGTGGATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggctttgcaaatggatttatttcatgggaaacctttc-tatagccactaattctgctgatattattacttgatatatgtttgtatctataaactg-

upper sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 2

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcactcttat----cacttatatacgca-gtttctcacctaggagatgttggatgtggttttc--ttactctacaaaggagaaggacaacaactttt
 ||||||||||  || || |||||||| || || | |||||| ||||||||||| || || |||||||||||| |||||||||| || |||||||| |||||| ||  ||  ||| || |    |||||  ||    | |    |  | | |   ||||| |   || | |    ||| |||  ||        || | ||      
AGAGGTTGCAACAAAATATCCTGGAATCAAGTACAGTGAAATTATTGTGGACAATTGCTGCATGCAGCTTGTTTCAAAGCCTGAGCAGTTTGATGTCATGgtatgtgaatatactattgtatagcactttaattgagatgcaaattgcttggtcaatgtttgtcatgttctgtaattattct-taagatttcctgatagca------

upper sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgta------cgtatattca-ctcttatcacttatatacgcagtttctcacctaggagatgttg--gatgtggttttcttactctacaaaggagaaggacaa--caactttt-----------------------------------
|||||| || || ||||| || |  || || ||||| ||  |||||||||| || || ||||||||||||||  | |||||| ||||||||||||| ||||||      ||||| |    |||   |  ||   |     ||||  |  |   |   ||| |   ||  || | ||  |     |  |    |||     |  ||| || |                                   
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag

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|71762747|gb|DR960684.1|DR960684

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT

EST: gi|113829317|gb|DW952549.1|DW952549

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAA
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAA

EST: gi|91052495|gb|EB162913.1|EB162913

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT

EST: gi|76923155|gb|DV169360.1|DV169360

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT

EST: gi|74233555|gb|DT641469.1|DT641469

EST:     AACTGTTGTATGCAGCTTGTTTGCAAA-CCTGAACAAATTTGATGTTATG                         GTCACCCCAAATCTTTATG
genomic: AACTGTTGTATGCAGCTTGTT-GCAAAGCCTGAACAA-TTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATG

EST: gi|71763037|gb|DR960974.1|DR960974

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT

EST: gi|71446644|gb|DR827694.1|DR827694

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATC
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATC

EST: gi|89755627|gb|DY685981.1|DY685981

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT

EST: gi|71433820|gb|DR814870.1|DR814870

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATCTTTATGGGCA-TCTGGTGGCTAATGTAGCTGCAGGTAT
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGG-CAATCTGGTGGCTAATGTAGCTGCAGGTAT

EST: gi|76284647|gb|DV024215.1|DV024215

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT

EST: gi|71439696|gb|DR820746.1|DR820746

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTAATG                         GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT

EST: gi|71433819|gb|DR814869.1|DR814869

EST:     ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATG                         GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT
genomic: ACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATT

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: 47 (upstream exon), 49 (downstream exon)
Score: 104

TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatat ... ccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgtacgtatattcactcttatcacttatatacgcagtttctcacctaggagatgttggatgtggttttcttactctacaaaggagaaggacaacaactttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggagaa