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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacaattatttttcaccttatatgaagctttctcatgaagttttcaccagtgaggaagttcccatgcctatctatttgtgtttctaattgtttctggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC

Basic information

species Zea mays
transcript GRMZM2G163658_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163658_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g38850.1 (Oryza sativa), 3'ss of exon 9
gtattacaattatttttcaccttatatgaagctttctcatgaagttttcaccagtgaggaagttcccatgcctatctatttgtgtttctaattgtttctggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC
             |||| ||||| ||| ||||||     |||| | || |  ||  ||      |||   |||  |   |  ||||||||||   ||   ||||  |||||||||| ||||||||||||||||||||||| ||| | ||||||||||| ||||| |||||||| ||||| || ||||| ||| | || ||||| ||||
------------gttttaaccttgtat-aagcttcactctgaaatgttaattagaaag------ccctaacctgccacatcatgtttctaatgaatttgagttcatagGCTTTACTGGAAGCCATGGAGCAGCAATGTGTATCTGTGGCAAAGGCTGGCCTTGTGGCAAGTTTATCAGCCCGTACTTCTGTGCTAGCGGCTGCTAATC

upper sequence: GRMZM2G163658_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA19G36230.1 (Glycine max), 3'ss of exon 8
gtattacaattatttttcaccttatatgaagctttctcatgaagttttcaccagtgaggaagttcccatgcctatctatttgtgtttctaattgtttctggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC
         || || |      | |   || |  | || ||    || |  |  | |   | ||   |    || ||       |  |      ||         ||||||||||| || || |||||||| || ||||| |||||||||||||| ||  | ||||||||||| ||| |  | ||||| || || || |||||||| |
-------gtttgttctctggtgtctggcaatcaatttcttg----ttactactttaatatattttaaacttttacctgaaaccttaacgtgaaattgtaataatacagGCTTTACTCGAGGCGATGGAGCAACAGTGTGTCTCTATTGCAAAGGCGGGATTAGTAGCAAGTTTATCATCCAGGACTTCTGTCTTAGCGGCTGCAAACC

upper sequence: GRMZM2G163658_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G09660.1 (Arabidopsis thaliana), 3'ss of exon 9
gtattacaattatttttcaccttatatgaagctttctcatgaagttttcaccagtgaggaagttcccatgcctatctatttgtgtttctaattgtttctggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC
                              | ||| || |   |       || |     | |||  |||   |  | ||| |  ||       |  ||      ||||| || || ||||| ||||| || |||||||| ||| ||||||||||||| |||||||| ||| | |||||||||||||| ||  | ||||| |||||||
------------------------------gttttttcttatcggcaatgtcatt-----acttctgatgttgacatttttctcattacttacatcactttgcaacagGCGTTGCTAGAAGCAATGGAACAACAATGTGTCTCTGTTGCAAAGGCTGGGCTTGTAGCTAGTCTATCAGCTCGAACTTCTGTTATAGCAGCAGCAAATC

upper sequence: GRMZM2G163658_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv08s0040g03290.t01 (Vitis vinifera), 3'ss of exon 9
gtattacaattatttttcaccttatatgaagctttctcatgaagttttcaccagtgaggaagttcccatgcctatctatttgtgtttctaattgtttctggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC
                     |    |||    |  ||||  |  | ||    |      | ||  || | | |   |||| |  || | |  ||||      ||||| || | || |||||||||||||| || ||||| ||| ||||||||||||| ||||| |||||||| ||||| |||||||| || || ||||| |||||||
------------------gtttggcctga---ctaatcattgatgtatcgtttgacctctaattgtcaagaccacacatttctaattttga--gtttac----ctcagTCTCTTCTAGAAGCCATGGAGCAACAGTGTGTCTCTGTTGCAAAGGCTGGACTTGTGGCAAGTTTATCAGCACGAACTTCTGTCTTAGCAGCGGCAAATC

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|60355947|gb|DN222920.1|DN222920
EST:     GTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAG                         GCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT
genomic: GTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAGgtattacaat ... tggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT
EST: gi|32942785|gb|CF047604.1|CF047604
EST:     GTGGAATATGCTGTATTGATGAGTTTGATANAATGTTTACAGAGCATCAG                         GCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT
genomic: GTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAGgtattacaat ... tggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT
EST: gi|32934840|gb|CF039652.1|CF039652
EST:     GTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAG                         GCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT
genomic: GTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAGgtattacaat ... tggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT
EST: gi|60339901|gb|DN206874.1|DN206874
EST:     GTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAG                         GCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT
genomic: GTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAGgtattacaat ... tggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT
EST: gi|32942784|gb|CF047603.1|CF047603
EST:     GTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAG                         GCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT
genomic: GTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAGgtattacaat ... tggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGT

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), 48 (downstream exon)
Score: 96

GTGCCATGGTCCTTGCTGATCGTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAGgtattacaat ... tggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 19

GTGCCATGGTCCTTGCTGATCGTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAGgtattacaat ... tggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 52

GTGCCATGGTCCTTGCTGATCGTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAGgtattacaat ... tggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 22

GTGCCATGGTCCTTGCTGATCGTGGAATATGCTGTATTGATGAGTTTGATAAAATGTTTACAGAGCATCAGgtattacaat ... tggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaggaagttcccatgcctatctatttgtgtttctaattgtttctggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC
                                ttctaat  putative branch site (score: 22)
                                      ttgtttct  CT-rich tract
                   tatctattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattacaattatttttcaccttatatgaagctttctcatgaagttttcaccagtgaggaagttcccatgcctatctatttgtgtttctaattgtttctggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC