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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTGAAGAGGACGCTTGACGTGGAGGAGGAGGTGGTGGACGGCGACGAGGACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgagatttccgtgctgctgctgcatttgccgcgtgggcgctcaagtccttggcttctgaacgcctgccgtcatcttgcccatttgcag

Basic information

species Zea mays
transcript GRMZM2G006714_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006714_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g18960.1 (Oryza sativa), 5'ss of exon 1
---ACCTGAAGAGGACGCTTGACGTGGAGGAGGAGGTGGTGGACGGCGACGAGGACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgagatttccgtgctgctgctgcatttgccgcgtgggcgctcaagtcc------ttggcttctgaacgcctg-ccgtcatcttgcccatttgcag-------------
   || ||||||||    | || |||||||| |||||||| ||||||||||||||||||||||||| |   || || ||||||||||| || || ||| || ||||||||| | |  | |     |   ||||||  ||  |  |  ||   |         |||| ||||||  | ||| | | | | ||| || ||  |               
TGGACTTGAAGAGGGTTTTGGAGGTGGAGGAAGAGGTGGTCGACGGCGACGAGGACGAGCTCGCCTCC---CCGGAGGCCAAGCGCCGGCGAACTTTCATCAAgtgagtgaaaatggcattgcatttgggcattt--cggttaagttcttgggattcatgagttgggttctgactgactgactgacgttttgtcccttgtcgttttcattgtgcag
















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|26559614|gb|CA831849.1|CA831849
EST:     GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGA                         TAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
genomic: GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
EST: gi|71300570|gb|DR786336.1|DR786336
EST:     GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGA                         TAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
genomic: GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
EST: gi|71327838|gb|DR800549.1|DR800549
EST:     GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGA                         TAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
genomic: GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
EST: gi|148931931|gb|EC875155.2|EC875155
EST:     GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGA                         TAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
genomic: GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
EST: gi|149014237|gb|EE043797.2|EE043797
EST:     GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGA                         TAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
genomic: GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
EST: gi|148986918|gb|EE030728.2|EE030728
EST:     GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGA                         TAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
genomic: GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
EST: gi|148944745|gb|EC889886.2|EC889886
EST:     GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGA                         TAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
genomic: GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
EST: gi|87157821|gb|DY402610.1|DY402610
EST:     GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGA                         TAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
genomic: GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
EST: gi|22715528|gb|BU197812.1|BU197812
EST:     GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGA                         TAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC
genomic: GACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCC

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 3 RNA-Seq libraries.


Block sizes: 22 (upstream exon), 48 (downstream exon)
Score: 7

ACCTGAAGAGGACGCTTGACGTGGAGGAGGAGGTGGTGGACGGCGACGAGGACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCCCAAGCTGGAGCCATTTCTGCGCAGAGTC


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 6

ACCTGAAGAGGACGCTTGACGTGGAGGAGGAGGTGGTGGACGGCGACGAGGACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCCCAAGCTGGAGCCATTTCTGCGCAGAGTC


Block sizes: 31 (upstream exon), 39 (downstream exon)
Score: 7

ACCTGAAGAGGACGCTTGACGTGGAGGAGGAGGTGGTGGACGGCGACGAGGACGAGCTCGCCTGCTGTCCCGACGCCAAGCGCCGCCGGACGTTCGTCGAgtgagtgaga ... ccatttgcagTAGCTCGATGCAGGAGGCCATTGGCGCGCAGTACATGCAGAGGCATCTGCCCAAGCTGGAGCCATTTCTGCGCAGAGTC