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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagtcctgtctgtatagtaaacgtgaacctgtaccatgatatatctcattcttattttctgcatttgttactactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGTTCTGGCAATGCTTTGGAAAGATTACTCGCCTTGGAACTCGAGCTTGCAG

Basic information

species Zea mays
transcript GRMZM2G179421_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179421_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g21940.1 (Oryza sativa), 3'ss of exon 10
----gtacgagtcctg-tctgtatagtaaacgtgaacctgtaccatgatatatctcattcttattttctgcatttgttactactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGTTCTGGCAATGCTTTGGAAAGATTACTCGCCTTGGAACTCGAGCTTGCAG
    | | |  |||   | | | | |||    | ||| || ||    ||     | |   |  | ||    || ||  |||  | ||||||||||| |||||    || |||||||| |||||||||||||||||||||||||||||||| ||||||||| |||| || ||||||||||| || ||||
gtatgcatgtctccccctttctgttgtaccattaaacatgaactggcatggcatttaccttattcttgctaatatggcact-ttctagGCAAATGAACATTTAAGGAGCATTTTTCCTTCATTTAAAGAGCTTCCTGGTTCTGGCAATGCCTTGGAAAGAGTACTTGCTTTGGAACTCGAACTAGCAG
















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|22545689|gb|BU098048.1|BU098048
EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
EST: gi|26558065|gb|CA830300.1|CA830300
EST:     TGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGN
genomic: TGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
EST: gi|120479870|gb|EH210656.1|EH210656
EST:     AAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: AAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
EST: gi|211190020|gb|FL186110.1|FL186110
EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCACTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
EST: gi|32945711|gb|CF050530.1|CF050530
EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
EST: gi|60343676|gb|DN210649.1|DN210649
EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
EST: gi|32936531|gb|CF041350.1|CF041350
EST:     CATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
EST: gi|78021778|gb|DV490165.1|DV490165
EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
EST: gi|211190018|gb|FL186108.1|FL186108
EST:     CTGACCCATCACTCARTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCAT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCAT

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: 189

ACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGTTCTGGCAATGCTTTGGAAAGATTACTCGCCTTGGAACTCGAGCTTGCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 84

ACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGTTCTGGCAATGCTTTGGAAAGATTACTCGCCTTGGAACTCGAGCTTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

ACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGTTCTGGCAATGCTTTGGAAAGATTACTCGCCTTGGAACTCGAGCTTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 153

ACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGTTCTGGCAATGCTTTGGAAAGATTACTCGCCTTGGAACTCGAGCTTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacctgtaccatgatatatctcattcttattttctgcatttgttactactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGTTCTGGCAATGCTTTGGAAAGATTACTCGCCTTGGAACTCGAGCTTGCAG
                                              ctacttt  CT-rich tract
                       attcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgagtcctgtctgtatagtaaacgtgaacctgtaccatgatatatctcattcttattttctgcatttgttactactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGTTCTGGCAATGCTTTGGAAAGATTACTCGCCTTGGAACTCGAGCTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT