ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag

Basic information

species	Zea mays
transcript	GRMZM2G148323_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 10

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacata-ttacataaacgtttta------tctgggcttgataaatattttcctttctacag-------------------------------------------------------------------------------
|||||| ||||||||||||||||| |||||||||||||||||||| ||||||||||||  ||||||||||||||||||||||||||||||||||||||||||||  |||   ||| | |||   |  | |||||      | |||    |   ||| |   | | |  |                                                                                  
TTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAAGAACCTGTGCTTTTTGAGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagcatcttggacagaattattgatgcattttaggcctgtttggaacagtggaatgtcagcatgttgaggaattgcaccatttaatgcaaaattcctgtgttccaaacaagtccttaaactgaatttgataaatcttttcttttccacag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatatt--ttcctttctacag---------------------------------
||| || |||||||||||||| ||||||||||||||||| ||||| ||||||||||||  ||| ||| | |||||||| ||||| ||||||||||| |||||   |  |   |  | ||   |  ||   || | ||  ||||    || ||  |        |||                                  
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctggaatatgatattctaatctagtcagta

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag--------------------------------
 || || |||||||| ||||| || |||||||||||||| |||||||||||||| |||   || ||||| || |||||  | ||||||||||||||||||||   |  |  | | | ||       | |  |   |   |||| |     ||      ||| |||                                
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA19G43790.1 (Glycine max), 5'ss of exon 10

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgtt--------ttatctgggcttgataaatattttcctttctacag---------------------------
||| || |||||||||||||| ||||||||||||||||| ||||| ||||||||||||  ||| ||| | |||||||| ||||| ||||||||||| |||||   |  |   |  | ||   ||    ||        || | | |  ||||| |  | |  | ||  |                               
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaatgttttttttatttattgtttgcccttgtattgtgttgatgagaagtcacattagttggaatatgatatgctaatctagtctgtagt

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G36530.1 (Glycine max), 5'ss of exon 10

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacat-----------attacataaacgttttatc-tgggcttgataaatattttcctttctacag-----------------------
||| || ||||| |||||||| || |||||||||||||| ||||||||||||||||||  ||||||||| || ||||| ||||| ||||||  ||| |||||      |   |  |           |||   | | | |||| || | |  ||| |    | |  |||||     |                       
TTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTTTTTGAGGACATATTGTGTCAGATAATTGACATGATTAAACCTGAGgtttgcctttccatctttcttttgatgattgtttgatctttttttcattgtgttgttgtgaaataacctttgcctggaaaagaaagtacaactctagtga

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G32500.1 (Glycine max), 5'ss of exon 10

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag--------------------------------
 || || |||||||| ||||| || |||||||||||||| |||||||||||||| |||   || ||||| || |||||  | ||||||||||||||||||||   |  |  | | | ||       | |  |   |   |||| |     ||| |   ||| |||                                
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgttttactcctctgcagtatagcaagtggtaactgtcctacgtttgcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G30930.1 (Glycine max), 5'ss of exon 10

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtaga--ttctcatacatattac-ataaacgttttatctgggcttgata-aatatttt----cctttctacag---------------------------
||| || |||||||||||||| || ||||| |||||||| |||||||||||||| |||  ||||||||| || ||||| ||||| ||||||  ||| |||||     ||  ||||  | ||   || |  |||| ||||    |   |    | || |       ||  |||                            
TTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAAGAGCCTGTGCTCTTTGAGGACATATTGTGTCAGATAATTGACATGATTAAACCTGAGgtttgcctttccatatttcttttgatgattgtttgatcttctatcattgtggtgttgtaaaattgttggacaagtgacctcaataatttaaggggggggg

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 5'ss of exon 9

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataa-atattttcctttctacag---------------------------------------------------------------------------------
 || || || ||||| |||||  |||||||||||||||| |||||| |||| |||||   ||| || ||||| ||||||||||||||||| ||||| |||||  |     ||   | ||   |     || | |||    |    || |||| |  |  || ||||                                                                                 
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaatatgtctcttgttt---ttttctttctatattaaggaagatatatgacagtc-acagaagtagtttgggttcccagtttttctttctgactcttgcgattttgtcttgtgtttgattgttttttatttccttccacag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 10

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttt---tatctgggcttg----ataaatattttcctttctacag-------------------------------------------------------------
 || || || ||||| |||||  |||||||||||||||| |||||| |||| |||||   ||| || ||||| ||||||||||||||||| ||||| |||||  |     |||  | ||   |     |||   ||| | |  | |    | || || |||   |||  |||                                                             
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaatatatctcttgttttcttctttctatatttagtatagtcacagaagtagtttgtgttcc-cagttttctttctgagtcttgtgattttgttttgtgtttgattgttttttatttccttccacag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 5'ss of exon 11

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgt-agattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag--------------------
 || || |||||||||||||| |||||||| |||||||| ||||||||||| || |||  ||| || ||||| |||||  |||| ||||||| ||||||||| |     |  | | ||        |  |    | |     |  | |  | |  |   | | |||                    
CTTTTATGAGGAGCAATTGCATCGAATGGAATGCATGGCCCAAGAGCCTGTACTATTTGAGGATATCTTATGTCAGATAGTTGACATGATTGCACCAGAGgtcacggcttttttcgtacccagatcatctcccgtgttctagtagttagcaataactcattttcagggcatgatttttgcttgcag

upper sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcataca-----tattacataaac-gttttatc--tgggcttgataaatattt--tcctttctacag--------------------------------------------------
||| |||||||||||| | || || |||||||||||||| || |||||||| ||||||  ||| ||  | || || ||||  |||||||| ||||| |  |||     |     |     |  |||||     | || |    | | ||  ||   | |    | | ||  || |                                                  
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag

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|23199690|gb|BU582255.1|BU582255

EST:     TATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGG-GTAAACTCTCAGGA
genomic: TATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA

EST: gi|87156079|gb|DY400868.1|DY400868

EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAT                         AATGAGAGCTATTTAATTCTACAGGACTT
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTT

EST: gi|83279222|gb|DV943230.1|DV943230

EST:     TATGCCAGATGATTGATATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA

EST: gi|23199745|gb|BU582310.1|BU582310

EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGCTATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA

EST: gi|211505069|gb|FK974737.1|FK974737

EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA

EST: gi|26560172|gb|CA832407.1|CA832407

EST:     TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAG                         AATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA
genomic: TGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGA

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), 48 (downstream exon)
Score: 323

TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTAACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAA

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 224

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 247

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG