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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattgtggctactttacctgaacactatgcatattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA

Basic information

species Zea mays
transcript GRMZM2G117064_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 4
gtgtgtttgcaacaaataccca-gtgcccaggaaagtgtttattgtggctactttacctgaacactatgcatattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
|| ||||   |  | || || | |    | |    |||       ||   ||||| | | ||||  |   || | ||||||| |||||||||||||||||| |||||||| ||||| |||||||| || ||||| |||||||| || ||||||||||| ||||| |||||||| |||||||
gtatgttacgataatatgccaaagcaatctgtgctgtgaagcccatgataacttttctttaacaacaccaatttattgaagGATGATGAAAGAGGCATGCGGTGGTTCTATTCTGGTGACATTGGACGTTTGCATCCAGATGGTTGCCTTGAAATTATTGACCGTAAGAAGGACATAGTCA

upper sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
----------------gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattgtggctactttacctgaacactatgcatatttt----gaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
                 | | |||  |    ||     | |   ||  |||     |  ||    | |  |  |    ||| || |  ||||    |||||||||||||||||| ||| | ||||| ||| |||| ||||||||| |  | || ||||||||||| |||||||| || || || || ||||| || || |
ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaagctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA

upper sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
----------------gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattgtggctactttacctgaacactatgcatatttt-----gaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
                 | | |||  |    ||    || |   ||  |||     |  ||    | |  |  |    ||| |  |  ||||     ||||||||||||||| || ||| | ||||| ||| | || ||||||||| |  |||| ||||||||||| |||||||| || ||  | || ||||| || || |
ttgtttgttttattttatttattt-tattttatgtggagggaggagagaaggtaaaaaggtacaaattacatgtttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA

upper sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S186_65V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------------------------gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattg--tggctactttacctgaacactatgcata-----ttttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
                                                                                             |    || |  || |  | | ||  |   | ||| | | |||  | | ||  | |    |   || ||  |      | |||||||| |||||||| | || ||||||||||||| | ||||||||||| |  || |||   ||||| ||| |||| || || ||||||||||| || || || |
gtgttttttttattccaaatgtttatttcactaaaggttctagttcgttgacacgcggcgatttattactctcaaataaaatcattttaagacgaacgtggatgaagtttctactgttctctacagt-tatgttggatagttatgtcataacagttctttgtcttggccttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTTCACGAGGATGGTTGTGTTGAGATCATTGACCGCAAGAAAGACATCGTAA

upper sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ26722 (Selaginella moellendorffii), 3'ss of exon 8
gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattgtggctactttacctgaacactatgcatattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
           |||| |   ||||  ||  ||| | ||| ||   |  || ||    |            | || |||||||||| || || |||||| ||||||||||| |||| |||||||| |  || || || ||||| ||  | |||||| | ||||| |||||||| || || |
---------gtacaacttttcagtttccttgaa-gcgttcat---gtttaattcgttt------------ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTA

upper sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ27012 (Selaginella moellendorffii), 3'ss of exon 8
gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattgtggctactttacctgaacactatgcatattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
           |||| |   ||||  ||  ||| | ||| ||          |||  ||           | || |||||||||| || || |||||| ||||||||||| |||| |||||||| |  || || || ||||| || || |||||| | ||||| |||||||| || || |
---------gtacaacttttcagtttccttgaa-gcgttcatg--------cttaattgggt------ttttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTCCATCCCGATGGTTGCCTGGAAATTGTAGACCGGAAGAAGGACATTGTTA

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|26456038|gb|CA827621.1|CA827621
EST:     TAACTAAAGGCTACTTCAAAAATGAAGCAAAAACAAATGAGGTGTACAAG                         GTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTG
genomic: TAACTAAAGGCTACTTCAAAAATGAAGCAAAAACAAATGAGGTGTACAAGgtgtgtttgc ... tattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTG
EST: gi|60347937|gb|DN214910.1|DN214910
EST:     TAACTAAAGGCTACTTCAAAAATGAAGCAAAAACAAATGAGGTGTACAAG                         GTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTG
genomic: TAACTAAAGGCTACTTCAAAAATGAAGCAAAAACAAATGAGGTGTACAAGgtgtgtttgc ... tattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTG

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), 49 (downstream exon)
Score: 77

AACCGATTCACCAATGCCTCGGGGTGAAATAGTTATTGGAGGTCCAAATGTAACTAAAGGCTACTTCAAAAATGAAGCAAAAACAAATGAGGTGTACAAGgtgtgtttgc ... tattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 28

AACCGATTCACCAATGCCTCGGGGTGAAATAGTTATTGGAGGTCCAAATGTAACTAAAGGCTACTTCAAAAATGAAGCAAAAACAAATGAGGTGTACAAGgtgtgtttgc ... tattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 65

AACCGATTCACCAATGCCTCGGGGTGAAATAGTTATTGGAGGTCCAAATGTAACTAAAGGCTACTTCAAAAATGAAGCAAAAACAAATGAGGTGTACAAGgtgtgtttgc ... tattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 149

AACCGATTCACCAATGCCTCGGGGTGAAATAGTTATTGGAGGTCCAAATGTAACTAAAGGCTACTTCAAAAATGAAGCAAAAACAAATGAGGTGTACAAGgtgtgtttgc ... tattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccaggaaagtgtttattgtggctactttacctgaacactatgcatattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
                                            atattttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattgtggctactttacctgaacactatgcatattttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG