Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattcagtcttttggctttcttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaag

Basic information

species Zea mays
transcript GRMZM2G088231_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088231_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 4
TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattca-----------gtcttttggctttct-tgctttttatttgctatttagga-gtgtgtgatgtgacagtaat--gcattttctctgttttaaaacaattaaaag
 ||||||||||| || |||||||||| ||| ||||| ||||||||||| || |||||||||||||||||||| |||  ||||||||||||||||||||||||||    |||           ||||||  ||||||| | |||  |   |  ||||| |   | |||   |||   ||| ||     ||||  |   || |||| || |  |||
ATCTGGCACTTCGGAGAATACAAAGGTTGTCATTGATCATGGGGCTGTACCAATATTTGTGAAGCTTCTTGGTTCTTCTAGTGATGATGTTCGTGAGCAGgtatccgatcatctcctgacttgtctttgtgctttctgtacttccttgatattattttgattgagtgcattgttggagttattaatgtttttacctcttgaaaaaaaattgaag

upper sequence: GRMZM2G088231_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G04430.1 (Glycine max), 5'ss of exon 4
TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtattt--attcagtcttttggctttcttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaag
 ||||| ||||| || ||||| ||||  || ||||| |||||||| ||||| |||||||| ||||| ||| | ||    |||||||||||||| |||||||||| |  || ||    | |||   |  ||   || | ||| | |  |    ||   ||  | ||   ||| |     |||||   |   |          
ATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCAGTTCCGATATTTGTCAAGCTACTTAGTTCGCCCAGTGATGATGTTCGGGAGCAGgtatgttgatgcatgaatgtggtagtgctgacatt-acttgttttgaaattttggccgagcttaccagaatactaaaactctgaaattccag---------

upper sequence: GRMZM2G088231_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G03430.1 (Glycine max), 5'ss of exon 4
TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattcagtcttttggctttcttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaag
 ||||| ||||| || || || ||||  || ||||| |||||||| |||||||||||||| ||||| ||| | ||   ||||||||||||||| |||||||||| | |    |    ||  | | | ||| |  |    || ||||    |   |||  ||| | | |   ||| |||    ||  |            
ATCTGGGACTTCTGAGAACACTAAGGTGGTAATTGATCATGGGGCAGTTCCTATATTTGTCAAGCTACTTAGTTCACCTAGTGATGATGTTCGGGAGCAGgtatgt-tatgtttgaatgcatctgtagctgtaca---actttttaattttac-tgaactgaaaatta---attctctgaaattccag-----------

upper sequence: GRMZM2G088231_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0005g01100.t01 (Vitis vinifera), 5'ss of exon 4
TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattcagtcttttggctttcttgctttt-tatttgctatttaggagtgtgtgatgtgac--agtaatgcatt------ttctctgttttaaaacaattaaaag---------------------------------
|||||| || |||||||| || |||| ||| || || ||||| || ||||| || ||||||||||||||||| ||    | ||||||||| ||||| ||||||| |||| |  |   || |    |         || |  | || | | || ||   ||   |  ||| |    |       |||  ||  |  ||   || |  |                                  
TTCTGGAACATCAGAAAACACCAAGGTTGTAATAGATCATGGAGCAGTTCCGATTTTTGTGAAGCTTCTTGGTTCCCAAAATGATGATGTCCGTGAACAGgtatatattaaaacagatgacaggttcatccccgcatgttttcttgatgtgtttgcattgcagctcagtcagttgtcaaatagttcattgcctataagtgatgaggaatttgagctttttagttttgccttttttctgtag

upper sequence: GRMZM2G088231_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv05s0077g01430.t01 (Vitis vinifera), 5'ss of exon 4
TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattcag---tcttttg--gctttcttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaag-------
|||||| || ||||||||||| ||||  || ||||| ||||| || || || |||||||||||||| ||||| |||   |||||||||||||| ||||||||  |||||      |  ||||  ||    ||     ||     || | ||  | |   ||   | |||   || |    | | | | | ||| |  |||  |        
TTCTGGGACATCAGAAAATACCAAGGTGGTAATTGATCATGGAGCAGTGCCAATATTTGTGAAGCTACTTGGTTCTCCAAGTGATGATGTTCGGGAGCAGgtgcttatttgaaatttgtttgaagcccgttttaagattgcagactgtatatcatttattggcataacatagattcgaggt-tttatatgaaatcctttaccaaaatgtag

upper sequence: GRMZM2G088231_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 5'ss of exon 4
TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattcagtcttttggctttcttgctttttatttgctatttagg--agtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaag--
|||||| || || || || || ||||  || ||||| ||||||||||| ||  | |||||||| |||||||| |||   ||||||||||||||||| ||||||  ||||  |         || ||  ||  | || |  | |||||   ||| |||  | | | | || |||||||| | |   |        ||  ||   
TTCTGGGACATCTGACAACACTAAGGTGGTAATTGATCATGGGGCTGTCCCGGTGTTTGTGAAACTTCTTGGTTCTCCAAGTGATGATGTTCGTGAACAGgtacatattttgaagaaca--ttcctacctgctaatatagtttttagtttagtttgtcttttta-attattgcatttttttttggtatgcttgtttggaatgt

upper sequence: GRMZM2G088231_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S43_141V6.1 (Physcomitrella patens), 5'ss of exon 5
TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattcagtcttttggctttcttgctttttatttgctatttagga-gtgtgtgatgtgacagtaatgcat----tttctctgttttaaaacaattaaaag
 || || || || ||  | ||    | ||| ||||| ||||||||||||||||| |||||  |||||||  | |||  |||||| |||||||||||||||||||  ||| | |  ||| |   | || ||  |||  ||| |  |     |  | | ||| || |||  ||| |    ||||| | |  |  | || |  |   
ATCCGGAACATCTGATCACACTCGTGTTGTGATTGAGCATGGGGCTGTTCCTATCTTTGTTCAGCTTCTGAGCTCTCCTAGTGACGATGTTCGTGAGCAGgtatgaattgaatgattttgggatattactgcttaactgccaggtgttctgcatctaatg-gatagttttgcttcagatttctatctggtgtatcactgca---

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|32858412|gb|CD998093.1|CD998093
EST:     ATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: ATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
EST: gi|71440662|gb|DR821712.1|DR821712
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
EST: gi|211385914|gb|FK983423.1|FK983423
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGA
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTT-GGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGA
EST: gi|28987202|gb|CB351514.1|CB351514
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGG
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGG
EST: gi|149111962|gb|EE191122.2|EE191122
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
EST: gi|87151836|gb|DY396625.1|DY396625
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
EST: gi|76021460|gb|DT948630.1|DT948630
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
EST: gi|78179900|gb|DV550273.1|DV550273
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGA
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGA
EST: gi|211385909|gb|FK983418.1|FK983418
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGGCTTTGGGTAATGTTGCTGGCGATT
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGG-CTTTGGGTAATGTTGCTGGCGATT
EST: gi|18963328|gb|BM660373.1|BM660373
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
EST: gi|22490161|gb|BU050084.1|BU050084
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
EST: gi|211383281|gb|FK983411.1|FK983411
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGGCTTTGGGTAATGTTGCTGGGCGATTCTCCGAAGTGC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGG-CTTTGGGTAATGTTGCTGG-CGATTCTCCGAAGTGC
EST: gi|18963326|gb|BM660372.1|BM660372
EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC

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: 751

TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 260

TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 244

TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 430

TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattcagtcttttggctttcttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG