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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatggcatatctcagtgtctattcctatacttacacatgtatcagaaacttctgtttgctgtgtattttcctggacgagtat...

Basic information

species Zea mays
transcript GRMZM2G166035_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 4
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatg----gcatatctcagtgtctattcctatacttacacatgtatcagaaacttctgtttgctgtgtattttcctggacgagtat---
|||||||||||||||||||||||||||||| ||||||| ||||| ||||| ||||| |||||||||||||||||||| ||| ||| || ||| ||  | |||||||         |||  ||     ||||  |||||   | | ||  |  || |   | | ||  |      | |  || |  |  ||     | |   |     
GATGCTGGCTCAACTGCCTCAACAGCTATTCTTGTAGGCGATCGCTTGCTGGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcactaaatctaatgtgtgtaacatacttcagttagtgt-ccagtgttttcctctatgtccaa------tttcagcaggatgcttgagaaggcatttgctgt

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G06250.1 (Glycine max), 5'ss of exon 5
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatggcatatctcagtgtctattcctatacttacacatgtatcag-aaacttctgtttgctgtgtattttcctggacgagtat--
||||| || |||||||| || || |||||| | || ||||| || |||||||||||||||||||| ||||| ||||||||||| |  |  || ||  | ||||||  |     | | | |    ||||    |  |  || | || |  ||   || ||||   | || | |||| | |   ||||    ||      |||  
GATGCAGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGACCGCTTGCTTGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgtaagctttataca-tatatgcatgcatgcatgcatacatctatctatttatctttagacatgtgtt-gttaattattaat-tgtgttgttattg

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 5
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatggcatatctcagtgtctattcctatacttacaca-tgtatcagaaacttctgtttgctgtgtattttcctggacgagtat-
|||||||| |||||||| || || || ||| |||| ||||| ||||||||||||||||||||||| || || ||||||||||| |  |  || ||| | ||||||  |   | | ||   |   ||||   |   |   |||  |     |  || || || |     |   ||||    || ||||   |    ||   | 
GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgtagccttatagtcttatattgtaa-atacgttctaagttgcatgcaatgcattatttg-tatggtttcacatgaatttagttttctgatcctt

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G12220.1 (Glycine max), 5'ss of exon 4
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaag---tttaccgtcgtaacatggcatatctcagtgtctattcctatacttacacat-gtatcagaaacttctgtttgctgtgtattttc-ctggacgagtat
|||||||| |||||||| || || || ||| |||| || || ||||||||||||||||||||||| || || ||||||||||| |  |  || ||| | ||||||   | || | |  ||   | | || | | | |    |||| ||     |||||| |||| ||  | |  |||||    || |||||   |  || | || 
GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGCGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggcttgtagctttttagtcttgtat-tgttacta--cattcttagttgcacacattgtattagtta-tattgtttcacatgaattttagttttactaata-

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 4
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagt---ttaccgtcgta-acatg-gcatatctcagtgtctattcctatacttacacatgtatcagaaacttctgtttgctgtgt-attttcctggacgagtat
|||||||| |||||||| || || |||||| | || ||||| || |||||||||||||||||||| ||||| ||||||||||| |  |  || ||  | ||||||    ||| | |  || |||   |||| | |   | | | |   |||  ||| |||||| |    || |  |   ||   |||  |||   | |||      
GATGCTGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGACCGCTTGCTTGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgttagctttatacacacatgcatgtatacatctatctatttatctttagacatgtgtagttaattattaactgtgttgttgtttaatttgac------

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 5'ss of exon 5
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatggcatatctcagtgtctattcctatacttacacatgtatcagaaacttctgtttgctgtgtattttcctggacgagtat-----
|||||||| ||||| || |||||||| ||  | || ||||| ||||| |||||||||||||| || || ||||||||||| || |  | ||| ||  | |||||   |       |   ||   | | ||   | | | ||     | ||  |     || ||||  ||  |          |       | | |   ||     
GATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGACCGTTTACTTGTTGCAAATGTAGGGGACTCTAGAGCTGTAATATGCAGAGGTGGCAATGgtaatgcttgttcatttttattatagaact---ttttttttgggggatttgaatggagattagaaggtt--gaaaaaaagaaaaaaaaaagaatggagattagaa

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G10740.1 (Arabidopsis thaliana), 5'ss of exon 5
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagttta--------ccgtcgtaacatggcatatctcagtgtctattcctatacttaca----catgtatcagaaacttctgtttgctgtg--tattttcctggacgagtat------------------------------------------
|| ||||| || ||||| || ||||||||| |||| ||||| |||||  |||||||||||||||| |||||||||||||||||    | ||| ||| | ||||| |||         ||||  | || |  | | | |   | |   |   |||  ||  |     | |||    | |  | ||| ||        | | || || |  |||||                                          
GACGCTGGTTCTACTGCGTCTACAGCTATTCTTGTTGGTGACCGTTTAGTTGTTGCAAATGTTGGTGATTCTAGAGCTGTTATCAGCAGAGGCGGAAAAGgtaaatttctatgagatccgttatgacttatctttttttgtttttggtggatatcattgtaatgttaagtaagcaatatctttgtatggcaccaccaatatcatgtagtagtatcctgatagataataccttttttcataaatctgtaccttgcag

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G24940.1 (Arabidopsis thaliana), 5'ss of exon 4
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatggcatatctcagtgtctattcctatacttacacatgtatcagaaacttctgtttgctgtgtattttcctggacgagtat
|||||||| |||||||| || ||||||||| | || ||||||||||| |||||||| |||||||| ||||| ||||||||||| | |   || ||| | ||||  ||||  | | |    | |  ||  ||| || || ||  |||   |  | || | || ||||    |        |||  | |  | |        
GATGCTGGTTCAACTGCTTCCACAGCTATTCTCGTTGGTGATCGTTTACTTGTTGCTAATGTTGGTGATTCCAGAGCTGTTATATGTCGTGGCGGAAATGgtacttttattgacat--ttttgattaagtca-tgactcttggtatctattgaaatct-tctgaaatgaat-----tcatgtgctcttgtag--------

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 5'ss of exon 5
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatggc-atatctcagtgtctattcctatacttacacatgtatcagaaacttctgt-ttgctgtgtattttcctggacgagtat
|||||||| ||||||||||| || |||||  |||| ||||| |||||||| |||||||||||||| || || ||||||||||| |  |  || ||  | |||||| |  |    ||  |||    || | |     | | ||  |  |        | ||||  ||  ||   | |||  | | ||||   ||       | 
GATGCTGGATCAACTGCCTCCACCGCTATCCTTGTTGGTGACCGTTTGCTGGTTGCAAATGTTGGGGACTCCAGAGCTGTTATCTGCAGGGGTGGTAATGgtaagat--ctagtgtgtcatttttatttttggaaatttttttgtgcatcagagtttctatcgtaattttgaatcttgaagagcatttatatgactttcaaa

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
lower sequence: PP1S225_37V6.1 (Physcomitrella patens), 5'ss of exon 4
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatggcatatctcagtgtctattcctatacttacacatgtatcaga-aacttctgtttgctgtgtattttcctggacgagtat-
||||| || ||||||||||| || |||||| | || || ||||||||||| ||||| ||||| || ||||| || ||||||||||  |  | |||||  ||| |    |  ||       | || |     | | |    |   | ||  |  |||  |  ||  | |   | |      || ||| |  ||      | | 
GATGCAGGATCAACTGCCTCCACGGCTATTTTGGTGGGAGATCGTTTGCTCGTTGCTAATGTAGGCGATTCAAGGGCTGTTATTTGCATCGCAGGACGAGgtgataagatggtgtctctgtagcttgaactattattc--tttaacaccaaaccatccaggagttagccattttgaatcttggattatattgacttcttttg

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|19350739|gb|BM895271.1|BM895271
EST:     TGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
EST: gi|6826953|gb|AW330596.1|AW330596
EST:     TGTTGCAAATGTTGGAGATTCTAGAGCTGNTATTTCTAAAGGAGGACAGG                         CAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
EST: gi|31359010|gb|CD443367.1|CD443367
EST:     TGGTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGGCANG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 509

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 589

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 558

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 350

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatggcatatctcagtgtctattcctatacttacacatgtatcagaaacttctgtttgctgtgtattttcctggacgagtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA