ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtattaatcattcttttcttaccacccatatactggatgtataatgaaatatatgtatcattcataaacatgtattttttgcag

Basic information

species	Zea mays
transcript	GRMZM2G007188_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 5'ss of exon 2

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtattaatcattcttttcttaccacccatatactggatgtataatgaaatatatgtatcattcataaacatgtattttttgcag
 || || ||||||||||||||||||||||| ||| ||||||| |||||||||||||||||||| ||||||||   ||||||||||||||| | |  |||||   |    |  ||  | ||| || ||||||||      | | ||||  || | |||||| | |  ||||
TCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCTgtaagtatcagt--ttcttaattatttattcacttgctgaat-tataatga------tttctcatggatcaccatgtaatct--gcag

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G49870.1 (Arabidopsis thaliana), 5'ss of exon 2

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta-atcattcttttcttaccacccatatactggatgtataatgaaatatatgtatc-----attcataaacatgtattttttgcag-----
|||||||||||||||||| ||||||||||| ||| |||| || |||||||| || || ||||||||||| ||     |||| |||||||| | ||  |||  || | |    |  | ||     |  || |||     |  | |||     ||   ||  | | | |||||    |     
CCTCTTCTTCAAGCAAGAAATGGAGCTTTCTTTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCAgtaagtataatatgcttcccttttgatattctctttaacacttagatgatggtggttggggatctgatgatgtctactcttatctttttacttgtttag

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G67560.1 (Arabidopsis thaliana), 5'ss of exon 2

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtattaatcattcttttcttaccacccatatactggatgtataatgaaatatatgtatcattcataaacatgtattttttgcag
|||||||||||||||||| ||||||||||||||| |||| || |||||||| || || ||||||||||| |||    |||| ||||||| ||  | | |        |   || | |  |        |||||    |   |  | | | |   ||| |   || | |||
CCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCAgtaagtagtatgcttccccaaaaatcgttccctctttttttctctaaatgactcgttgatggcttccttttgcattt-ccttgtccag

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv00s0601g00030.t01 (Vitis vinifera), 5'ss of exon 2

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtat-taatcat-----tcttttcttaccacccatatactggatgtataatgaaatatatgtatcattcataaacatgtattttttgcag
|||||| |||||||| || ||||||||||| ||| |||| || || ||||||||||||||||||||||| ||     |||| |||||||  |||||||     || ||   ||     | | | |    | | |   |  |    ||   ||||   ||   | |  |||| |   
CCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaataatcatgtatgtcattctctaatggtcctttcccatttatttggggctaatgctgacacattggaaactgtattgttttag---

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0091g00970.t01 (Vitis vinifera), 5'ss of exon 2

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtattaatcat------------tcttttcttaccacccatatactggatgtataatgaaatatatgtatc---attcataaacatgtattttttgcag-
|||||| ||||| ||||| |||||||| || ||| |||| || || ||||| || |||||||||||||| ||    ||||| |||||||    ||||            | || | |||         |      | | |  |     |   ||  |   |||| |       |  || |||||  
CCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCAgtaagtaaagttcatgcaaaatgtgagttttcttttattgtttccctctcctttctttggtttggcactggtggctaaattcctttgtggat-cttgttgcaag

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S6_409V6.2 (Physcomitrella patens), 5'ss of exon 3

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtattaatcattcttttcttaccaccca---tatactggatg--tataa------tgaaatatatgtatcattca--taaacatgtattttttgcag
||| ||||||||||||||||||||||| ||  || |||| || || || |||||||||||||| ||||| ||    ||||| ||| ||||   | ||| | | ||   ||  ||   |||   | |||  |||||      |  ||  | || | | |     | |    | ||| ||| || 
CCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCGgtatgtatctgtaattttctcctccgcaagcaagctatggcgcatgcctataaacgctgtacaagttgtggaccgtcagggtcagttcggattatttaca-

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S103_13V6.1 (Physcomitrella patens), 5'ss of exon 2

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtattaatcattcttttcttaccacccata-tactggatgtataatgaaatat--atgtatca--------ttcataaacatgtattttttgcag-
||| || |||||||||||||||||| | || ||| ||||| | ||||||||||| ||||| || || |||||   |||||| ||  ||     | |  |  ||||        ||| | ||   |  | | ||   | |  | | | ||        | | |||| ||   |     |||| 
CCTATTTTTCAAGCAAGAGATGGAGTTGTCTTTGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCGgttcgtgcctctaaccccattctatttctgtatacttctatttacacactgtcttgttcacgcaccagtttggattccctaaatatagctccccagcagc

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ23242 (Selaginella moellendorffii), 5'ss of exon 2

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtattaatcattcttttcttaccacccatatactggatgtataatgaaatatatgtatcattcataaacatgtattttttgcag
||||||||||||||||||||||||| | ||| |  |||| || ||||| ||||| || || || ||||| |||||||| |||||||||   ||    ||| || |   | | | |   ||| |||  ||  ||  |    |                             
CCTCTTCTTCAAGCAAGAGATGGAGTTATCAGTAATAGGACTACAAAAGGCTGGCAAGACGTCCCTTGTCAACTCCATCGCTgtaagttccaagttctctcttttc-tcgctctttcgctg-atggttatcgattttctag-----------------------------

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ25249 (Selaginella moellendorffii), 5'ss of exon 2

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtattaatcattcttttcttaccacccatatactggatgtataatgaaatatatgtatcattcataaacatgtattttttgcag
||||||||||||||||||||||||  | ||| |  |||| || ||||| ||||| || || || ||||| |||||||| |||||||||   ||    ||| || |   | | | |   ||| |||  ||  ||  |    |                             
CCTCTTCTTCAAGCAAGAGATGGAATTATCAGTAATAGGACTACAAAAGGCTGGCAAGACGTCCCTTGTCAACTCCATCGCTgtaagttccaagttctctcttttc-tcgctctttcgctg-atggttatcgattttctag-----------------------------

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|71306605|gb|DR789463.1|DR789463

EST:     CCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: CCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211136580|gb|FL266974.1|FL266974

EST:     GGTAGGGCTCCAAAATGCTGGGAAAACGATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: GGTAGGGCTCCAAAATGCTGGGAAAAC-ATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211135637|gb|FL266963.1|FL266963

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|13178422|gb|BG349680.1|BG349680

EST:     GTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: GTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|76012951|gb|DT940121.1|DT940121

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211135642|gb|FL266968.1|FL266968

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211136581|gb|FL266975.1|FL266975

EST:     GGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCCATTGCT                         ACTGGAGGTTTTTAGTGAGGATATGATCCCTACTGTAGGATTCCAATATG
genomic: GGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACT-CCATTGCTgtaagtatta ... ttttttgcagACTGGAGG-TTTTAGTGAGGATATGATCCCTACTGTAGGATT-CAATATG

EST: gi|211135639|gb|FL266965.1|FL266965

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGCGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|67012163|gb|CO440912.1|CO440912

EST:     TGGTAGGGCTCC-AAATGCTGGG--AA-A-CACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211136576|gb|FL266970.1|FL266970

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTYTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|13178421|gb|BG349679.1|BG349679

EST:     GTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: GTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211135631|gb|FL266957.1|FL266957

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|71306606|gb|DR789464.1|DR789464

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|76012952|gb|DT940122.1|DT940122

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211135634|gb|FL266960.1|FL266960

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211135635|gb|FL266961.1|FL266961

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|13178420|gb|BG349678.1|BG349678

EST:     GTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: GTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|71332505|gb|DR803215.1|DR803215

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|148969394|gb|EE020186.2|EE020186

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|83278732|gb|DV942740.1|DV942740

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|16377996|gb|BI992228.1|BI992228

EST:     GGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: GGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211136583|gb|FL266977.1|FL266977

EST:     TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT                         ACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

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: 111

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtatta ... ttttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAGGTTACCAAAGGGAATGTGACGATAAAATTGTGGGATATTGGAGGCC

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 36

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 50

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 86

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtattaatcattcttttcttaccacccatatactggatgtataatgaaatatatgtatcattcataaacatgtattttttgcag

- - - - - - - - - - - - - - - - - - - - - - -  ATGCTG