Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagcatattttatgctctctattcgggatatgaatatcagagtttatgcatttctcacactgctggtctgtgtaacttatttgactttccatatgttcctag

Basic information

species Zea mays
transcript GRMZM2G108477_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108477_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g44150.1 (Oryza sativa), 5'ss of exon 4
CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagcatattttatgctctctattcgggatatgaatatcagagtttatgcatttctcacactgctggtctgtgt-aacttatttgac----tttccatatgttcctag
|| || |||||||| |||||||||||||| || |||||||||||| |||||   |||||| | |  | | ||| || |   |||     ||||     | | |||    || ||    || || |   |||||||||  |     ||   | || |   ||
CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTGgtaaatcagcatctctcttaccctc-atcc---atactgccatca---cctcttcatcctgcatacaatgggcctataccaacttattttccatggctttgttgtgctttcag

upper sequence: GRMZM2G108477_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G00510.2 (Glycine max), 5'ss of exon 4
----------------------------------------------------CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagcatatttt-atgctctctattcgggatatgaatatcagagtttatgcatttctcacactgctggtctgtgtaacttatttgactttccatatgttcctag
                                                     | ||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||    | |      | | |   | |      |||  ||   |    ||   ||| | ||  |   ||| ||  |  |    | ||    || || |||||     
CTTCTGGCTTCATAACAGTTTAGCAACCACTGTTTCCTGCTTTTTGTTTCAGTTGAAAGAATACATTGATGACACCGAAGATTTCATCAACATTCAACTGgtttgttttctttcccccagggttcatgtcaattttatttatcctaattattggtcatgtttcttatgtctgatc-atacatgcaaatta---ttgcacatgtt-----

upper sequence: GRMZM2G108477_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G00510.1 (Glycine max), 5'ss of exon 5
CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagcatatttt-atgctctctattcgggatatgaatatcagagtttatgcatttctcacactgctggtctgtgtaacttatttgactttccatatgttcctag
 | ||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||    | |      | | |   | |      |||  ||   |    ||   ||| | ||  |   ||| ||  |  |    | ||    || || |||||     
TTGAAAGAATACATTGATGACACCGAAGATTTCATCAACATTCAACTGgtttgttttctttcccccagggttcatgtcaattttatttatcctaattattggtcatgtttcttatgtctgatc-atacatgcaaatta---ttgcacatgtt-----

upper sequence: GRMZM2G108477_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G44820.1 (Glycine max), 5'ss of exon 5
CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagcatatttt-atgctctctattcgggatatgaatatcagagtttatgcatttctcacactgctggtc-tgtgtaacttatttgactttccatatgttcctag
 | ||||| ||||| |||||||| ||||| |||||||||||||| |||||  |    | |      | | |   | |      |||  ||   |    |    ||| | ||  ||  ||| || |   |    || || | |   |||          
TTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTGgttcgttttctttcccccagggttcatgtcaattttatttatcctaattatctgtcatgtttcttacgtctgatcatacatgcaataatttattgcacat----------

upper sequence: GRMZM2G108477_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G16010.3 (Arabidopsis thaliana), 5'ss of exon 6
CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgta-tgccagcatattttatgctctctattcgggat--atgaatatcagagtttatgcatttctcacactgctggtctgtgtaacttatttgactttccatatgttcctag
 | || |||||||| |||||||||||||| ||||| |||||||| |||||| | ||   | |||  ||  ||   |   |  ||  ||  | ||  |||  |   ||    |||  |||     || |  ||  | |                      
TTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTGgtaatacctcaaaattccatcttccacagctgatattaatccagatt-gagaatgcacaagagtcatgctgaaaacctcttcaatatctgcag------------------

upper sequence: GRMZM2G108477_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G80900.1 (Arabidopsis thaliana), 5'ss of exon 4
CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagcatattttatgctctct---attcgggatatgaatatcagagtttatgcatttctc--acactgctggtctgtgtaacttatttgactttccatatgttcctag
 | || |||||||||||||| || ||||| ||||||||||||||  |||||| ||   | || ||   || | |   ||     || ||  ||  | |  ||| | || |     | | | ||||  | || |                            
TTAAAGGAGTACATCGATGATACCGAAGATTTCATCAACATTCAATTGgtataccttgaaatcttgatcttttttagatatcttatttgcttagaaaaccttaagaatctgctgaaaatttctggaatttgcag---------------------------

upper sequence: GRMZM2G108477_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0018g00600.t01 (Vitis vinifera), 5'ss of exon 4
CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgc-cagcatattt--tatgctctctattcgggatatgaat--atcagagtttatgcatttctcacactgctggtctgtgtaacttatttgactttccatatgttcctag
|| || || ||||| |||||||| ||||| ||||| ||||||||||||||| |    |  | |||  |||    |   ||| |   | | ||  |  | ||   |   ||| ||   |    || | | |    | ||||||| ||| | |||        
CTGAAGGAATACATTGATGACACAGAAGATTTCATTAACATTCAGCTGgtacgtgttgtttctttcttatatgtttggttccgagaaagtattaagaaaagaaaaaaaattgctattaaaaatgatttct----catatttgattttac-tat--------

upper sequence: GRMZM2G108477_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S423_14V6.1 (Physcomitrella patens), 5'ss of exon 4
CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagcatattttatgctctctattcgggatatgaat---atcagagtttatgcatttctcacactgctggtctgtgtaacttatttgactttccatatgttcctag
 | || ||||| || ||||||||||| |||||||||||||| |||||||||    |  | | ||   |||||||  ||  |   | | |   |  ||| |  ||| | | |  |  ||  |  |  |  |   |     ||| |  |||          
TTGAAGGAGTATATAGATGACACTGAGGACTTCATCAACATACAGCTGgta----attacaattccagctctcttgtcctgcattcactctaactagattaaatggaatccagatccttttaatacgattgtgtatcaagacataacatgct-------

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|148950017|gb|EC895546.2|EC895546
EST:     CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTG                         GACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA
genomic: CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagc ... atgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA
EST: gi|60396116|gb|DN228985.1|DN228985
EST:     CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTG                         GACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA
genomic: CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagc ... atgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA
EST: gi|211306497|gb|FL467488.1|FL467488
EST:     GTACATCGATGACACTGAAGACTTCATCAACATTCAGCTG                         GACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA
genomic: GTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagc ... atgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA
EST: gi|26457168|gb|CA828751.1|CA828751
EST:     CGCTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTG                         GACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA
genomic: CGCTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagc ... atgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA
EST: gi|78544782|gb|DV622280.1|DV622280
EST:     CGCTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTG                         GACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA
genomic: CGCTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagc ... atgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCA

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: 44 (upstream exon), 49 (downstream exon)
Score: 53

CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagc ... atgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCAACATTTGTTGTGGCCATTTTCGGAGTGGTTGCTGGGATATTCGGGATGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 103

CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagc ... atgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCAACATTTGTTGTGGCCATTTTCGGAGTGGTTGCTGGGATATTCGGGATGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagc ... atgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCAACATTTGTTGTGGCCATTTTCGGAGTGGTTGCTGGGATATTCGGGATGA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 91

CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagc ... atgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCAACATTTGTTGTGGCCATTTTCGGAGTGGTTGCTGGGATATTCGGGATGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTGgtatgccagcatattttatgctctctattcgggatatgaatatcagagtttatgcatttctcacactgctggtctgtgtaacttatttgactttccatatgttcctag

- - - - - - - - - - - CTGAAG
- - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - CAGCTG