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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccatgtattccttagttcttaaactgttttctcttttccctcgcagataacatttattttcatttacatactgtag

Basic information

species Zea mays
transcript GRMZM2G056393_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 5'ss of exon 15
CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccatgtattccttagttcttaaactgttttctcttttccctcgcagataacatttattttcatttacatactgtag-------
||||||||||||| || |||||||||||||| |||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| | || |      | ||  || |  | | ||  |     |||||| | | |||   ||| ||| || |         
CTGATGGTAAATTTGAGTTTGATAACATGATCATTGGACAAGCAATTCCTTCAAACTTCATACCAGCAATTGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccatgtctcccatcacgtgttaaaagtctattttgtttgcagagtgataacttgtgtttgtgtttccattctatgcactgcag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 15
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 5'ss of exon 15
CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagt--ccatgtattccttagttcttaaactgttttctcttttccctcgcagataacatttattttcatttacatactgtag------------------------------------
|| | |  || || |||||||| ||||||||| |||||||||||||||| ||    ||||| |||||||| ||||| ||||| || ||||||   || ||||||||   | ||   ||   | |||||   || | |    || | | |      |  |  || ||||  || |   | ||| |                                    
CTAAAGAGAAGTTTGAATTTGAAAACATGATTGTTGGACAAGCAATTCCGTCTGGTTTTATTCCAGCAATTGAGAAAGGTTTCAAAGAAGCTGCAAACTCgtgagtgatcttggtctctcaaattctttgtctttctcaatttctacttt-----tttctcttgttttggttgaggaaatgttgttgtaagtgatagtgaaacgccctattccattgcag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 15
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 5'ss of exon 15
CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtc-catgtattccttagttcttaaactgttttctcttttccct-------------cgcagataacatttattttcatttacatactgtag
|| | |  ||||| || ||||| ||||||||| |||||||||||||||| ||    ||||| |||||||| ||||| ||||| || ||||||   || ||||||||    |   |  || | ||  |    |   |  |  |||   |              | |  | ||| | |    |  |     | || ||
CTAAAGAGAAATTTGAGTTTGAAAACATGATTGTTGGACAAGCAATTCCGTCGGGTTTTATTCCAGCAATTGAGAAAGGTTTCAAAGAAGCTGCAAACTCgtgagtgatcttcgtctctcaatttctcgttttcctcttgatttatttgaggaaatgttgttgtaagtgacagtgaaaccccctattccattgcag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 15
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 5'ss of exon 15
CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagt------ccatgtattccttagttcttaaactgttttctcttttccctcgcagataacatttattttcatttacatactgtag---------------------------------------------------------------------------
|      ||| || |||||||| ||||||||| | ||||||||  | || || || ||||| ||||| || |||||||||||||| |||||   ||||||||||||      |||| | ||  |   || ||      | |  ||||||   |   | ||   ||| || ||  ||   || || |                                                                             
CCACCACTAAGTTTGAATTTGAGAACATGATTGTAGGACAAGCTGTACCATCCAATTTTATCCCAGCCATTGAGAAGGGTTTTAAAGAAGCAGCCAATTCgtgagtggtttaccatttctttttctttttttttttcatctgatcttttttattataaatgg-attgatattttttctgattctatgcatgaacttttggtaactatcaaagaagtgtgaactattgttattagtattgatctgatttctcgtacttgtacag

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|84980317|gb|DW530666.1|DW530666
EST:     TAGAGAAGGGTTTTAAGGAAGCTTGCAATTC                         AGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
genomic: TAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
EST: gi|32932818|gb|CF037630.1|CF037630
EST:     TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAGGGAAGCTTGCAATTC                         AGGCTCGTTGATTGGTCATCCTGTTGAAAATGTAAGAATTGTATTGACTGA
genomic: TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
EST: gi|211184463|gb|FL030548.1|FL030548
EST:     TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTC                         AGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
genomic: TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
EST: gi|6194594|gb|AW146698.1|AW146698
EST:     TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTC                         AGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
genomic: TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
EST: gi|6020648|gb|AW065681.1|AW065681
EST:     TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTC                         AGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
genomic: TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
EST: gi|33093919|gb|CF053913.1|CF053913
EST:     TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAGGGAAGCTTGCAATTC                         AGGCTCGTTGATTGGTCATCCTGTTGGAAATGTAAGAATTGTATTGACTGA
genomic: TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
EST: gi|61119855|gb|DN560816.1|DN560816
EST:     AGAGAAAGGTTTTAAGGAAGC-TGCAAATTC                         AGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTG
genomic: AGAGAAGGGTTTTAAGGAAGCTTGC-AATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTG
EST: gi|69351603|gb|DR452190.1|DR452190
EST:     TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTC                         AGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
genomic: TCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
EST: gi|67017174|gb|CO445923.1|CO445923
EST:     CAAACTTTATACCAGCAATAGAGAAAGGTTTTAAGGGAAGCTTGCA-TTC                         AGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA
genomic: CAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGG-AAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGA

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), 49 (downstream exon)
Score: 154

CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGATGGGGCTTCACATCAGGTGGATTCCAGTGAACTTGCTTTTAAGCTAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGATGGGGCTTCACATCAGGTGGATTCCAGTGAACTTGCTTTTAAGCTAGCT


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

CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGATGGGGCTTCACATCAGGTGGATTCCAGTGAACTTGCTTTTAAGCTAGCT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 150

CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccat ... catactgtagAGGCTCGTTGATTGGTCATCCTGTTGAAAATTTAAGAATTGTATTGACTGATGGGGCTTCACATCAGGTGGATTCCAGTGAACTTGCTTTTAAGCTAGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGATGGTAAATTCGAATTTGATAACATGATTATTGGACAAGCAATTCCTTCAAACTTTATACCAGCAATAGAGAAGGGTTTTAAGGAAGCTTGCAATTCgtgagtccatgtattccttagttcttaaactgttttctcttttccctcgcagataacatttattttcatttacatactgtag

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