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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatgctttgtgtgacacgtagtcattttctggataatgagatctgctgctgccctgagcgtttgtcttcctgcgcctactgatcaggacatgtaatttcttttttggtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGATTGAAAATTTCATACTAGTAGGGTGTTACTAGTAGAACACGATGCAGGA

Basic information

species Zea mays
transcript GRMZM5G868757_T04
intron # 7
splice site 3'
intron type U2

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|166643495|gb|EG036618.1|EG036618
EST:     AGCAAGGTCCCATTTGCAAAAT                         GACATGGATGGTTAGAACTGCACGACAGTGTCACGGAGAACGGGACCAATG
genomic: AGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACG-CAGTGTCACGGAGA-CGGGACCAATG
EST: gi|4609963|gb|AI600802.1|AI600802
EST:     CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAAT                         GACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
genomic: CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
EST: gi|4804325|gb|AI666191.1|AI666191
EST:     CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAAT                         GACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
genomic: CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
EST: gi|60336794|gb|DN203767.1|DN203767
EST:     CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAAT                         GACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
genomic: CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
EST: gi|166472734|gb|EG227362.1|EG227362
EST:     CAAGGTACCCAATTTGCAAAAT                         GACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
genomic: CAAGGT-CCC-ATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
EST: gi|33094129|gb|CF054123.1|CF054123
EST:     CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAAT                         GACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
genomic: CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
EST: gi|33095168|gb|CF055162.1|CF055162
EST:     CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAAT                         GACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA
genomic: CTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGA

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), 37 (downstream exon)
Score: 17

CTTTCAGTTGAGGCGGAAACACCTGATCTTGTTGCTGTGTAATTTCACAGCTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGATTGAAAATTTCATACTAGTAGGGTGTTACTAGTAGAACACGATGCAGGA


Block sizes: 44 (upstream exon), 35 (downstream exon)
Score: 13

CTTTCAGTTGAGGCGGAAACACCTGATCTTGTTGCTGTGTAATTTCACAGCTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGATTGAAAATTTCATACTAGTAGGGTGTTACTAGTAGAACACGATGCAGGA


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 10

CTTTCAGTTGAGGCGGAAACACCTGATCTTGTTGCTGTGTAATTTCACAGCTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGATTGAAAATTTCATACTAGTAGGGTGTTACTAGTAGAACACGATGCAGGA


Block sizes: 47 (upstream exon), 36 (downstream exon)
Score: 13

CTTTCAGTTGAGGCGGAAACACCTGATCTTGTTGCTGTGTAATTTCACAGCTGTTACACTTCCGCGAGAGGCTTGGTCAGCAAGGTCCCATTTGCAAAATgtgagatgct ... gtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGATTGAAAATTTCATACTAGTAGGGTGTTACTAGTAGAACACGATGCAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcttcctgcgcctactgatcaggacatgtaatttcttttttggtgccctcagGACATGGATGGTTAGAACTGCACGCAGTGTCACGGAGACGGGACCAATGGATTGAAAATTTCATACTAGTAGGGTGTTACTAGTAGAACACGATGCAGGA
               tactgat  putative branch site (score: 13)
                                              tgccctc  putative PPT
                            atgtaatttctttttt  TA-rich tract