ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatggaacattttcataattatcataccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag

Basic information

species	Zea mays
transcript	GRMZM2G114861_T01
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os04g53760.2 (Oryza sativa), 5'ss of exon 14

GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgta---gaatggaacattttcataattatca--taccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag
||||||||||| ||| || ||||||||||| || ||| | || |||||||| |||||| | |||||||||||||| || ||||||   |  |    ||| ||    | ||| |   ||   | |  | |   | | | |||||   ||  | | |||   | |  |        ||   || ||| |     || |   | |  |  | |      |   ||    |||  ||||    ||  |||||
GTCTGTGGGTAGGACCCAAATGAATGAACAATCTTCCCGGAGCCATTTTGTTTTCACACTGAAGATATCTGGATCAAATGAGgtactcgcttcacccatattttagaatattaatcacagtgctgaaactttacaaactggtcacaatattttttttttcattttca-----tgctaactaaacagaaccactgaaacttgagcaaatgt------atgtcactaattttcttttgatcttaatgcag

upper sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA12G34330.1 (Glycine max), 5'ss of exon 13

GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatggaacattttc--ataattatcataccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag
 |||||||| || ||||||||||||||||| || || ||||||||||||||||||||  |     ||| |||    || ||||||   | |    |  ||  | | | ||   |||| | |  |   | |   | | |   |    | | | |||| | || | || |  | | ||  |  |                                                               
ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGATTATATGGTGTAAATGAGgtatggttgtttctcctctgacagtaattgaaccatgtttcat--acactcaatagcaatctaacaagcattcaaattg-caaccaatcttgttctgctag--------------------------------------------------------------

upper sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA13G36230.2 (Glycine max), 5'ss of exon 14

GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatggaacattttc-ataattatcataccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag
 |||||||| || ||||||||||||||||| || || ||||||||||||||||||||  |    |||| |||    || ||||||   | |  |   ||  | ||| ||   |||| | |  |   | |     |     |    | | | |||| | || | ||      || ||  || |                                                              
ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgttctcctttgacaataattgaaccatgtttcat--acactcgataacaatctaacaagcattcaaattg-caac--ctgattgttctactag-------------------------------------------------------------

upper sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA12G16580.1 (Glycine max), 5'ss of exon 14

GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatggaacattttcataattatcataccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag
 ||||||||||| || |||||||||||||| || || ||||||||||||||||||||  |    ||||  ||    || |||||| |     |  |||   |  | |  ||| | | | | |             |||||     ||  |||||   |     |    |    ||  ||||| |   ||  |         | |||   |   | | |       ||||| ||||| || |||
ATCTGTGGGTAAAACCCAGATGAATGAACAATCATCAAGAAGTCATTTTGTATTCACTCTTCGAATATACGGTGTAAATGAGgtaaag----atgtttctcttttgacaataactaaaaccat------------gtcctatgtttagttttcaattt----ccatctcaaccttcaacaaacacactgact--------tgcatcacaatgcaacct-------attttatctttcttccag

upper sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA06G41600.1 (Glycine max), 5'ss of exon 13

GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatggaacattttcataattatcataccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag
 |||||||| || || |||||||||||||| || || ||||||||||||||||||||  |    ||||  ||    || |||||| |       ||||||     ||| ||  |||   |||     | |   || ||  ||| | || |||             ||  |  | |  || | |  |   ||  || |        | || |  | ||  ||   |  ||| ||||| || |||
ATCTGTGGGAAAAACCCAGATGAATGAACAATCATCAAGAAGTCATTTTGTATTCACTCTTCGAATATACGGTGTAAATGAGgtaaag------attttc-----tattatgacaatgacta-----aaaccatgttctatattcaattttt------------aatttccatctcaaccagtgatagacacactga--------cttgcgtca-caatgcaacctatttgtctttcttccag

upper sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT5G54670.1 (Arabidopsis thaliana), 5'ss of exon 14

GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgta--gaatggaacattttcataattatcataccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag
|||||| || |||||||||||||| || || || |||||||| |||||||| |||||  |||  || |||||   ||||||||||   |    | | | ||  |  |||    |      | |      ||| |     |    |  | ||||||  || |                                                                                    
GTCTGTAGGGAAGACTCAGATGAACGAGCAATCTTCCAGAAGCCATTTTGTTTTCACGCTAAGAATCTCTGGTGTTAACGAGgtactaaccaaaccgtctttcttcttacagaatgtttgttttgtgtgataaaccaaactggcttttttctttcttacag------------------------------------------------------------------------------------

upper sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 5'ss of exon 13

GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatggaacattttcataattatcataccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag
||||||||| || || ||||||||||| || || ||||||||||||||||| |||||  |   |||||||||   ||| |||||| || |     | |||||  |   |         | | |  | | || |  |  |||    ||| ||| |                 ||||  ||  |||||   ||                                                    
GTCTGTGGGCAAAACACAGATGAATGAGCAATCATCCAGAAGTCATTTTGTGTTCACTCTGCGGATATCTGGTGTTAATGAGgtataaag-----tcttcatggtgccctc-------tgtgctgatacattgatgctcttg-attatgttttaactctgttttctctttgtttttcacttatattgaccag---------------------------------------------------

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|211045020|gb|FL382451.1|FL382451

EST:     TTCACATTAAAGATATCTGGATCTAACGAG                         AACACAGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGG
genomic: TTCACATTAAAGATATCTGGATCTAACGAGgtagaatgga ... ttttttgcagAACACAGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGG

EST: gi|67019346|gb|CO448095.1|CO448095

EST:     CGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG                         AACACAGGCCANAATGTGCAAGGAGTCCTTNAACT-GATTGATTTANCTGG
genomic: CGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatgga ... ttttttgcagAACACAGGCCAAAATGTCCAAGGAGTCCTT-AACTTGATTGATTTAGCTGG

EST: gi|18167051|gb|BM336890.1|BM336890

EST:     TTTGTATTCACATTAAAGATATCTGGATCTAACGAG                         AACACAGGGCC-AAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGG
genomic: TTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatgga ... ttttttgcagAACACA-GGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGG

EST: gi|67014413|gb|CO443162.1|CO443162

EST:     TCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGNATCCTACCGAG                         AACACAGGCCANAATGTCCAAGGAGTCCCTTA-CTTGATTGATTTAGCTG
genomic: TCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGG-ATC-TAACGAGgtagaatgga ... ttttttgcagAACACAGGCCAAAATGTCCAAGGAGTCC-TTAACTTGATTGATTTAGCTG

EST: gi|18167204|gb|BM337043.1|BM337043

EST:     CGTCC-GAAGT-ATTTTG-ATT-ACATTAAAGATATCTGGATCTAAC-AG                         AACACAGGCC-AAATGTCC-AGGAGTCCTTAACTTGATTGATTTACCTGGG
genomic: CGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatgga ... ttttttgcagAACACAGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGG

EST: gi|78085386|gb|DV513779.1|DV513779

EST:     CGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG                         AACACAGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGG
genomic: CGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatgga ... ttttttgcagAACACAGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGG

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: 236

GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatgga ... ttttttgcagAACACAGGCCAAAATGTCCAAGGAGTCCTTAACTTGATTGATTTAGCTGGGAGTGAGCGTCTTGCTAAAAGTGGCTCCACAGGTGATCGCTTGAAGGAAA

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 87

Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 74

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 533

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatggaacattttcataattatcataccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag

- - - - - - - - - - - - - - - - - -  AGAAGT