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

gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG

Basic information

species Zea mays
transcript GRMZM2G453794_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
||||||||||||||||| ||| | || | | |  ||||||  |||  | || ||   |   || || |  || ||    |||||||| ||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||   ||||||||||||||||
gtaagtgcttttacataatatatattttctatttcatgag--tcatttcaagttacatactgtcaacatttggaa----ttcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 38
gtaagtgc-ttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
|||||  | ||||| ||   ||  |   |  ||      || ||||    ||   || ||    | || |           ||| || ||| ||  | ||||||||||| ||||| ||||||||||||||||| || ||  ||||  | ||||| || || ||||| || ||    ||||| || ||||| 
gtaagcccattttaaattaaataatgatttcttttgtcaagaatcaaactaa---gtatgacaatgatgc-----------tctatt-tagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACGTAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
gtaagtgc-ttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
|||||  | ||||| ||   ||  |     |||| | | | |||    | ||| |  || |    |     |||  |  | |       || ||  | ||||||||||| ||||| ||||||||||||||||| || || |||||  | ||||| || || ||||| || ||    ||||| || ||||| 
gtaagcccattttaaattaaataatg---atttctcgtcaagat----tcaaactaagtatgacaa-----tgatgctctattc-----agGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 37
gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
||||||     |||     ||  ||| | | |  | |||  |  |  | || |    || | |   ||    |    || |   || |||  |  | ||||| ||||||||||||||||| ||||| ||| | |||||||| ||| | ||||| || || |||||||||||   ||||||||| ||||| 
gtaagt-----tactaccaataatttttatcttccgtga--acaacttgaactcagatggaatccttattctattatttctgaattctagGATCCGCATGCATTATGGTCATCCAGATGTCTTTGACAGAGTATTTCATATTACACGTGGTGGTATCAGCAAGGCCTCTCGGGTCATCAATATTAGTGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 35
gtaagtgcttttacata-gtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttg--tagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
|||||| | ||||  || | | |   | | ||| |  | |  ||||  | |||||  |  ||  |    | ||||| ||||  |  ||   || ||  | ||||| ||||| ||||||||||||||||||||| |||| ||||||||| | ||||| || || |||||||||||    ||||| || ||||| 
gtaagttcatttaattaagcaagcaatttatttgatgtcat-atcattttaaatttgggataactggagc-tgaaatctttaataatggccagGGTTCGTATGCATTATGGCCATCCAGATGTTTTTGATAGAGTTTTCCATATAACACGAGGTGGTATCAGCAAGGCCTCTCGAGTTATCAACATTAGTGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
-------------gtaagt-----gcttttacatagtatgttttctgtttcacatg--aggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
             |||| |     | | | |  |||||||  || ||  | |  ||  | | |   | |  | |  || | |||  |||||   |        | || || ||||| ||||| ||||||||||| |||||||||||| | || || |||||||||||||| || || || ||  | ||       || ||| ||||||| 
aattatatgtgctgtaaatcgttagttctaatctagtatgactt-tgccttaggtgccaaggttt-cgatgacttcgtatggttgctacatatga--------tgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S145_49V6.1 (Physcomitrella patens), 3'ss of exon 36
gtaagtgcttttacatagt-atgttt-tctgtttca--catgaggatcagctaaaattgtgtgtagttaatacatga---aaccttttcttttg---tagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
 |  ||  ||    |  || ||| |  |  | ||||  |||   |   |  |   |||   || |||| ||   ||    ||||    | ||||   ||| ||||||||||||||||| || || ||||| |||||  | ||||| ||||| |||||||| || || |||||||| ||       || ||  | ||||| 
cttcgtatttcgctacggtcatgctcgtacgcttcaaacattctgcggaaatggtattcgatgaagtttatttctgctgtaaccgcaccatttgctgtagGGTGAGAATGCACTATGGACACCCGGATGTCTTTGACCGCATTTTCCATATCACAAGGGGAGGCATCAGTAAGGCATCGAAGCAGATTAACCTTAGTGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S13_132V6.1 (Physcomitrella patens), 3'ss of exon 37
-------gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagc--taaaattgtgtgtagttaatacatgaa--accttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
         ||          ||      || | | | | |  ||   | ||    |    ||  |  || ||| |     |   ||  | | ||||  |||||||||||||||||||| ||||||||||| |||||  | ||||| || || |||||||| || ||||| ||| | ||       |||||| | ||||| 
cctatccacaaa-atcggggaattccgatttgtttctattatctggaaaccaatagttccctttcgactatttagttagcaatttactgtgtgttttacagAGTGAGAATGCACTATGGGCATCCAGATGTCTTTGACCGCATTTTCCACATCACAAGGGGAGGCATTAGCAAGTCATCCAAGCAGATCAATCTTAGTGAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S18_300V6.2 (Physcomitrella patens), 3'ss of exon 16
---gtaagtgcttttacatagtatgttttctg-----tttcacatgaggatca-gcta--aaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
    |        |||    |    || | ||      | |  ||||   |||  |||  |||| |||   | || ||  || ||    | | || || || ||||||||||||||||| ||| ||||||| |||||| |||| ||||| ||||| || || ||  | || || || ||       |||||| |||||  |
gtcatggtcataattatcaggaccattatttgagaatctgcttatgaacttcatactagtaaatggtgcacaattcatg-attaatatatgtgttatgcagGGTGAGAATGCACTATGGACATTCAGATGTGTTTGATCGAATATTTCACATAACGAGAGGAGGTGTAAGCAAAGCATCAAAGCAGATCAATCTCAGTACG

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S40_186V6.2 (Physcomitrella patens), 3'ss of exon 22
----------------------------------------------------------------------------------------------gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
                                                                                              ||| | |   | |   | | ||       ||||         ||| | ||  ||   ||   ||     || ||  |   |  |  | || || |||||||||||||||||||| |||||||| ||| | || || || ||||||||||| || || || ||  | ||       |||||| | ||| | 
gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagc-tttcttgcacatgtcatcaaagtttcgatgactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
                                          | ||   |   |  ||  |  |  ||  ||  | |  || || |  || ||||||||||| || ||||||||||||||||| |||||||| || |||||||||||||| || |||||||| ||||||||   ||| || || ||||||
-----------------------------------------gtaagtctactcttggtagaacttgta-gtgttaacagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG

upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ05083 (Selaginella moellendorffii), 3'ss of exon 37
gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
                                        |  |  |||   ||| ||  |  |  ||  ||  | |  || || || || ||||||||||| || ||||||||||||||||| |||||||| || |||||||||||||| || |||||||| ||||||||   ||| || || ||||||
----------------------------------------gtacgtctattcttg-gtagaacttgta-gtgttaacagtttttatgcagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG

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|211477278|gb|FK976144.1|FK976144
EST:     GAGACAAGTTTTGTGACATTAGGACAGCGTGTTCTTGCTAACCCGCTGAA                         AGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATAT
genomic: GAGACAAGTTTTGTGACATTAGGACAGCGTGTTCTTGCTAACCCGCTGAAgtaagtgctt ... tcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATAT




















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: 187

TGTTTCCTCCCTGGCCTCATTTATGTCTAATCAGGAGACAAGTTTTGTGACATTAGGACAGCGTGTTCTTGCTAACCCGCTGAAgtaagtgctt ... tcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

TGTTTCCTCCCTGGCCTCATTTATGTCTAATCAGGAGACAAGTTTTGTGACATTAGGACAGCGTGTTCTTGCTAACCCGCTGAAgtaagtgctt ... tcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

TGTTTCCTCCCTGGCCTCATTTATGTCTAATCAGGAGACAAGTTTTGTGACATTAGGACAGCGTGTTCTTGCTAACCCGCTGAAgtaagtgctt ... tcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 154

TGTTTCCTCCCTGGCCTCATTTATGTCTAATCAGGAGACAAGTTTTGTGACATTAGGACAGCGTGTTCTTGCTAACCCGCTGAAgtaagtgctt ... tcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
                                        ccttttcttttgt  CT-rich tract
            taaaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA