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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgttttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcatacactgaaacatatccaaacttaa...

Basic information

species Zea mays
transcript GRMZM2G056975_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgttttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcatacactga-aacatatccaaacttaa----------------------------------------------------------------------------------
||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||| |||||||||||||||||| |||||||||||||||| |||| | || || |||               | | ||||| ||   || ||| ||  || ||||  |  || ||||  ||   || || ||||||                                                                                  
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatg--------------gaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag

upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 9
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgttttactaaaaagcacatgttgaggtat-tctgcccagatgtag-tgcttcatacactgaaacatatccaaacttaa----
|||||| |||||||||||||| || ||||| ||||| || ||| | ||||||||||| ||||| ||||| || |||||||| || ||| ||||||| |||||     ||||| | || || |||||| |  |    | | ||| || |  |   | |     |||| |  ||  | |   ||   |  |  | ||| ||  |    
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTACGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgt-----ctaaatc-taattctatgttatgttggttaccgcattttaatatccatatatttggatgcaaatggatgaggaaccatagtacctacaagctacaagtt

upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA17G09740.1 (Glycine max), 5'ss of exon 9
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtg--agccctaaaccatagttatatgttttactaaaaagcacatgttgaggtattctgcc-cagatg--tagtgcttcatacactgaaacatatccaaacttaa-
|||||| |||||||||||||| || ||||| ||||| |||||| | ||||||||||| ||||| ||||| || |||||||| || ||| ||||||| |||||   | || ||  | || ||||| |   |||||  |      || |  |  ||||| |   || |||  |   |   ||||  |   | ||  | |||  |  | 
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTATGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgtataaaccttattctat-gttatgt---ttactgcattttg-atatccatatattcggatacaaatggatgaggaaccata-gccatagcacctacaagttccag

upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 5'ss of exon 9
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaacc-atagttatatgttttactaaaaagcacatgttgaggtattctgc-ccagatgtagtgcttcatacact---gaaacatatccaaacttaa---------------------
|||||||||||||||||| ||| | ||||| |||||||||||||| ||||||||  | ||||| ||||| ||||||||||| |||||||| ||||| ||||| |    | | |  || ||  |   || | || ||    |  | || || | |      |||   | | || ||||||   |   ||| |   | |  |  |                       
AGAAGTTATTGAAGCACACTATCTGTTTGGGGCTGAATATGATGATATTGAGATCATAATTCATCCACAATCTATCATACATTCTATGGTCGAAACACAGgttaattgttatcttattgtcttggcttcttcttaa---tatgt-ttaagatgtcaaataccatcagaactgtttcatattttttagaagcggtttcttatgtcttctccacccctttctctccag

upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 9
lower sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgttttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcatacactgaaacatatccaaacttaa
 || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || || |||||        ||    ||||  ||| || |  | | | |  |    |       ||   || ||  ||                                
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgt--------aatatgagttgaatgcttcaacacacaactaacacag-------ctagtcaaatacag--------------------------------

upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 9
lower sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgttttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcatacactgaaacatatccaaacttaa
 || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || || |||||        ||    ||||  ||| || |  | | | |  |    |       ||   || ||  ||                                
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgt--------aatatgagttgaatgcttcaacacacaactaacacag-------ctagtcaaatacag--------------------------------

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|14206809|gb|BG840487.1|BG840487
EST:     AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAG                         GATTCATCTGTCCT
genomic: AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCT
EST: gi|32798103|gb|CD950339.1|CD950339
EST:     AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAG                         GATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
genomic: AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC

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: 53

AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 604

AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 467

AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 29

AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgttttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcatacactgaaacatatccaaacttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaaaa