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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttgctcccaactcctctgcgtatatgtagcttgcaagtacagtctgaagcgcgctgactgcagggggggtgtcctgtgcag

Basic information

species Zea mays
transcript GRMZM2G110834_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110834_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 5'ss of exon 11
CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttgctcccaactcctctgcgtatatgtagcttgcaagtacagtctgaagcgcgctgactgcagggggggtgtcctgtgcag--
 |||||  ||||||||||||| || ||||| ||||||||||| ||||| |||||| ||||||| ||| | ||||||||||||||||| ||||||| ||| |   || | ||    |  |  | |     ||  | ||  || ||          |        | || | |||| |   
GAAACCTGTTAAAAAGGTGGGGTCTTTCTGTTGGCTTTCCCTAGCTATTTGCATTTTGGAGCTTCTACTATGCATCAAGTTTGGACATGgtgagt-ttgatgtaaatttcttgatgctt--gcaagcaacatttgcatccttaaaattaaccgttctgaacacgttggcttgtgaacag

upper sequence: GRMZM2G110834_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT1G15110.2 (Arabidopsis thaliana), 5'ss of exon 12
CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtg-ttgctcccaactcctctgcgta---tatgta-gcttgcaagtaca--gtctgaagcgcgctgact--gcagggggggtgtcctgtgcag--
 |||||  | |||||||||||| | ||||| ||||| || ||||  |||||||| || || || || ||||||||||||||||||   |||  ||| || ||  ||  | |||||| |    ||| || | || ||  ||||  || || || | |   |||  |  |   || | |  |  | |   
AAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTGGTAGgtggttccttacacatgctctgccttagttatttatggttacagttacatagtgtggagagtgtaaacttggttgtatggttatgatacgaacag

upper sequence: GRMZM2G110834_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 5'ss of exon 12
CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgt--tgctcccaactcctc----tgcgtatatgtagcttgca-agtacagtctga--agcgcgctgactgcagggggggtgtcctgtgcag---------------------------------------------------
 |||||| | |||||||||||| | || || ||||||||||| ||||| |||||| | || || || || ||||||||||||||||| |||  ||    |  ||  ||  | |     ||   || |  || ||||  | |||    ||   | |  ||| |    ||    | ||||  ||  |                                                    
AAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATGgtttgttccctattctaaaagcattataatgaacatttcaagtttgcttattacctattggttaactggctaatca-agtattgatgtctagttgatgtgtaaaacttgcctgctgacatttgtgaactgttattttactcttaccag

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|42491818|gb|CK700864.1|CK700864
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|60397677|gb|DN230493.1|DN230493
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|166577869|gb|EG126841.1|EG126841
EST:     ATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGC
genomic: ATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGC
EST: gi|91869156|gb|EB400279.1|EB400279
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATTTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|84969395|gb|DW467833.1|DW467833
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|211076057|gb|FL474784.1|FL474784
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|6672167|gb|AW282342.1|AW282342
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|74231927|gb|DT639841.1|DT639841
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATTTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|71318559|gb|DR796040.1|DR796040
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATTTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|113841671|gb|DW967677.1|DW967677
EST:     CTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTACGTGGCTGATCACATTCTGGTCAGCA
genomic: CTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTT-CGTGGCTGATCACATTCTGGTCAGCA
EST: gi|76910092|gb|DV163696.1|DV163696
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|211529174|gb|FL238578.1|FL238578
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCACCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG

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: 43 (upstream exon), 48 (downstream exon)
Score: 65

CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 75

CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 34

CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttgctcccaactcctctgcgtatatgtagcttgcaagtacagtctgaagcgcgctgactgcagggggggtgtcctgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT