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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgtcggttctacaagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG

Basic information

species Zea mays
transcript GRMZM2G024151_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
gtaattgtcggttcta----caagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
|| | || |  ||||       || | |      |  || |   || |   | ||  |  | ||    ||| ||||     || ||||||||| || || || |||||||| ||||||||||||||||| ||||| || || ||||| ||||| ||||| || |||||||||||||||||||||
gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------gtaattgtcggttctacaagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
                                         ||| |||   | |      |  |||     |  |  |||       |  | | |         | |    |  || | ||||||||  | || || || ||  | || || || || |||||||| || || ||||| ||||| ||||| || |||||||| || |||||||||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgta--tgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------gtaattgtcggttctacaagcttgtgaattgtcttctata-gaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
                                                  ||| |||||      |    ||   | |||| |    |  | ||   |      |       | | | ||  || ||||||||  | || || || ||  | || || || || |||||||| || || ||||||||||| ||||| ||||||||||| || ||||| |||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtaattgtcggttctacaagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
      ||  |   | ||  ||||    || | |||| |       |   |   | ||   |  ||   || ||  | | ||||||| | ||||| || ||  | || ||||| ||||||||||| ||||| ||||| |||||||||||||| || || ||||| || || |||||||||
------gtacgca-tgcattcttgctcttttttttctgttttttt-tgcgagtcgctcttgctcaa---gacttgcttttgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtaattgtcggttctacaagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
            |   || || |      | |||| | |       |   |   | ||   |  ||   || ||  | | ||||||| | ||||| || ||  |||| ||||| ||||||||||| ||||| ||||| |||||||||||||| || || ||||| || || |||||||||
-----------gtacgcatgcattcttgctctcttttttctt--tttgcgagtcgctcttgctcaa---gacttgcttttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

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|211161694|gb|FL418712.1|FL418712
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|61117965|gb|DN558926.1|DN558926
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|61117966|gb|DN558927.1|DN558927
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|33097248|gb|CF057208.1|CF057208
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|60349962|gb|DN216935.1|DN216935
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAA                         GTCCTCGGTACG
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACG

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: 48 (upstream exon), 49 (downstream exon)
Score: 2083

CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 883

CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 960

CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 774

CCTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
                               ccctaaa  putative branch site (score: 774)
                                  taaaatgattttgtat  TA-rich tract