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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgttactgtattacatagttgtatcattgtatttgtatcaatgtgagtgtgtaggcttatggctttagcttttacatgaactatgcattccact...

Basic information

species Zea mays
transcript GRMZM2G028346_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028346_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 7
TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgttactgtattacatagttgtatcattgtatttgtatcaatgtgagtgtgtaggcttatggctttagcttttacatgaactatgcattccact--------
                ||||||||||| || ||||||||||||||||||||||||||||| |||||||| |||||||| || ||||||||||| || || ||||| |   |||  | |||| |         |   | | || | |   |    || |  | ||     |||    | ||  ||||| ||   |  || |        
---------------GCCTTTTGGTTGTGGAGTTATTCTTGGAGGTTATGATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaacactacagtacacaagaa----gtcaaactcgtcttaggctcttggtttttgttt----ttttcatctctatgtgaaccattattagcaattaaattgt

upper sequence: GRMZM2G028346_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G14330.2 (Glycine max), 5'ss of exon 6
TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttg-ttactgt-attacatagttgtatcattgtatttgtatcaatgtgagtgtg-taggcttatggctttagcttttacatgaactatgcattccact--------------------------
               ||||||||| || ||||| || || ||||||||||| ||||||||||||||| | |||||| | || || || || ||||||||||| || |  ||  ||| |||  ||||     ||      | | ||| | |     ||   | |   |     ||| |   || ||||   |||   |   |                            
---------------ACCTTTTGGATGTGGTGTCATACTAGGAGGTTATGACAGGGATGGACCACAGTTGTACATGGTTGAACCTTCCGGTGTTTCCTATgtgagctactttttgtcatttgatagcaacttccagacttctttataattacacatgcaattgatattcctttttggaagttccatgtggtatttttgtaatgatttgttcatttggtaattgttctag

upper sequence: GRMZM2G028346_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 6
TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgttactgtattacatagttgtatcattgtatttgtatcaatgtgagtgtgtaggcttatggctttagcttttacatgaactatgcattccact---------------------------------
               ||||||||| || ||||| || || ||||||||||| ||||||| ||||||| | |||||| | || || || || ||||| ||||| |||      | | |||  |  | | | | |  |   |   ||  | | | |    | ||   ||   ||   ||||  | |  | |||   |    |                                 
---------------ACCTTTTGGATGTGGTGTCATACTAGGAGGTTATGACAGGGATGAACCACAGTTGTACATGGTCGAACCTTCTGGTGTTTCTTATgtgagtatactttttgttatttgatagcaacttcctgact---tccttataattacacatgcaattgctattccttttttgaagttccatgtgctatttttgtaatgatatgttcgtttggtaattgttctag

upper sequence: GRMZM2G028346_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 6
TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgttactgtattacatagttgtatcattgtatttgtatcaatgtgagtgtgtaggcttatggctttagcttttacatgaactatgcattccact-
                |||||||| || || ||||||||||||||||||||||| |||||||| ||  | |||||||| || || |||||  | || |||||||||| || |||     | ||| | |      || | | ||  | | |||   | || | |  |       |   | | ||||| | |   | |  |  
---------------GCCTTTTGGCTGTGGGGTTATTCTTGGAGGTTATGATAGAGATGGACCTCAATTGTACATGATTGAACCATCAGGCATATCATATgtaagttatttctgc---ccgtagatat------gtgtcttta--agtatgaaattttacgttatttttccctgtcatcatatgaattctat-tcctgcag

upper sequence: GRMZM2G028346_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv08s0040g00410.t01 (Vitis vinifera), 5'ss of exon 6
TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgttact------gtattacatagttgta-tcattgtatttgtatcaatgtgagtgtgtaggcttatggctttagcttttacatgaactatgcattccact----------------------------------------------------------
               ||||||||| || || || ||||||||||||||||| || |||||||||||  | |||||| | || || || || ||||||||||| ||||| || |         ||  | || |||  | ||   || | |     | ||||  | ||  | | |  ||    || || || |   |  | |||    |                                                          
---------------ACCTTTTGGATGTGGAGTAATTCTTGGAGGTTATGACAGAGATGGACCACAATTGTACATGGTTGAACCTTCTGGTGTTTCCTATgtgagttgatatttggcataagttgtagagctgtggttatcaaatgtattctgttatgagcttttactcatgtatctactactctttca-gtcttcagaatttatgtggtggtgttatttgggaatttttttcattttgtgcttcttttttttttttggttctag

upper sequence: GRMZM2G028346_T02 (Zea mays), 5'ss of exon 1
lower sequence: PP1S72_57V6.4 (Physcomitrella patens), 5'ss of exon 8
TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgttactgtattacatagtt---gtatcattgtatttgtatcaatgtgagtgtgtaggcttatggctttagcttttacatgaactatgcattccact-------------
               |||||||||||     | ||| ||||||||||| ||| | ||||| || || ||||||||||| ||||| || || ||| |||||||||||| ||  | |  | ||        ||  |||| | ||  | |   | | || | | |      ||  | | | | |   ||  ||  | | || || |             
---------------ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCAACTTTACATGATTGAGCCTTCGGGTGTTGCCTATgtaagttattgttttcctccacccccaacgtgacattcttttcctgttcct-tcagaggggaattgcttgtttgttgatctggtatttacggtacgttacattgttgtggatgtag

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|211079760|gb|FK950720.1|FK950720
EST:     ATAGGGATGGGCCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTAT                         AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC
genomic: ATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgtt ... acttgaacagAAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC
EST: gi|32933640|gb|CF038452.1|CF038452
EST:     ATAGGGATGGGCCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTAT                         AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC
genomic: ATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgtt ... acttgaacagAAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC
EST: gi|211169213|gb|FL479845.1|FL479845
EST:     TTTACATGATAGAGCCCTCAGGAGTTTCCTAT                         AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC
genomic: TTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgtt ... acttgaacagAAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC
EST: gi|12969059|gb|BG266004.1|BG266004
EST:     ATAGGGATGGGCCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTAT                         AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC
genomic: ATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgtt ... acttgaacagAAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC

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: 46 (upstream exon), 49 (downstream exon)
Score: 174

TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgtt ... acttgaacagAAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgtt ... acttgaacagAAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 129

TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgtt ... acttgaacagAAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 120

TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgtt ... acttgaacagAAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTGTTATATCAGACCTTTTGGTTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGACCACAGCTTTACATGATAGAGCCCTCAGGAGTTTCCTATgtaagttgttactgtattacatagttgtatcattgtatttgtatcaatgtgagtgtgtaggcttatggctttagcttttacatgaactatgcattccact

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA