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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCTCCACCTCAAGTGGCAGCAGTTCCACCACCAGCTCCACCTGATGCTCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaagcaatgtgttgaactgctttattttgcgaagtaccatggattagtggtttgtttcttataggtgtatgttatttttttaactggtgttaag...

Basic information

species Zea mays
transcript GRMZM2G069916_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 6
CCTGCTCCACCTCAAGTGGCAGCAGTTCCACCACCAGCTCCACCTGATGCTCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaagcaatgtgttgaactgctttattttgcgaagtaccatggattagtggtttgtttcttataggtgtatgttatttttttaactggtgttaag--------
 || |  |||||||| ||||| |||| ||| |||| ||||| ||||||||||| ||||||||||| |||||||||||| | |||||||||||||||||||||||| |||| |  |       || |||||||   | |||||  ||| ||  | ||||  |||||| |  | |  |  |   |   | ||  | |  |||        
ACTCCAACACCTCAAATGGCATCAGTACCAGCACCTGCTCCCCCTGATGCTCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaagaaccgct-----ctactttatt--actaagtagtatgcatgcg-ggttgttttcttctgtgaggttactggctcagttacaagggccaagatatagtt

upper sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 5'ss of exon 6
---CCTGCTCCACCTCAAGTGGCAGCAGTTCCACCACCAGCTCCACCTGATGCTCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatgga--aagcaatgtgttg--aactgctttattttgcgaagtaccat-ggattagtggtttgtttcttataggtgtatgttatttttttaactggtgttaag
    | | |||| ||||   |  | ||| | || |   | |||| || ||| |||||||||||||||| ||||| ||||| || |||||||| ||||||||||||| |||  || |    | ||   | ||| ||| || |  |  ||   || | ||  || | |  ||   |    || |  ||  |      || ||  |||   
CAGGCAGTTCCAGCTCA---GCAACCAGCTGCAACTTTACCTCCGCCCGATCCTCGTACTCAAGAAATGATCAATGAAAAACTAAAGAAAGCAGAAGAGCTTGgtaaggagcaaacctcttattcgtatctgttttgttatatgtggtgatattgaatcggtagctctttaagttaccgtttcagtggtgcaa--aattgtggtt---
















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|67033512|gb|CO462261.1|CO462261
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACA-GGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|32832751|gb|CD972429.1|CD972429
EST:     TACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|32835473|gb|CD975151.1|CD975151
EST:     ACTCAAGAAATTATCAACGAAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: ACTCAAGAAATTATCAACG-AAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|60340812|gb|DN207785.1|DN207785
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|76920400|gb|DV168155.1|DV168155
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|32834150|gb|CD973828.1|CD973828
EST:     AATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: AATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|148952947|gb|EE152420.2|EE152420
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAAACA-GGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAA
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAA-CAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAA
EST: gi|71312972|gb|DR793008.1|DR793008
EST:     TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAG
EST: gi|149000973|gb|EE038213.2|EE038213
EST:     TCGTACTCAAGAAATTATCACCGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GTGAACCAGG-ATGGTTGATGAAGCTCAAAAAGCTT
genomic: TCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTT

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: 242

CCTGCTCCACCTCAAGTGGCAGCAGTTCCACCACCAGCTCCACCTGATGCTCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

CCTGCTCCACCTCAAGTGGCAGCAGTTCCACCACCAGCTCCACCTGATGCTCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 134

CCTGCTCCACCTCAAGTGGCAGCAGTTCCACCACCAGCTCCACCTGATGCTCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

CCTGCTCCACCTCAAGTGGCAGCAGTTCCACCACCAGCTCCACCTGATGCTCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... gttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCTCCACCTCAAGTGGCAGCAGTTCCACCACCAGCTCCACCTGATGCTCGTACTCAAGAAATTATCAACGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaagcaatgtgttgaactgctttattttgcgaagtaccatggattagtggtttgtttcttataggtgtatgttatttttttaactggtgttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT