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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttactgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactctaggctcagctggacatgggcttgtttctttgcttgcatgcatgtttcagttttttctccttgcagctgaatttaatctgcaactatgtaatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG

Basic information

species Zea mays
transcript GRMZM2G058948_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 10
gtgagtttactgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactctaggctcagctggacatgggcttgtttctttgcttgcatgcatgtttcagttttttctccttgcagctgaatttaatctgcaactatgtaatgagcaatt--tccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                  ||| ||||    || |  |  |  |||| ||  || | || | |  ||||         |||||| || |  |||| |   ||  | || |  ||| |||| | |  ||||||||||||| || ||||||||||||||||||||||||  ||| ||||||||||||||||||||||| ||||||||||||||||| ||||||||||| ||||
---------------------------------------------------------------------------------actgcacat----ttatagcccttgttgcctgtgtgct-cattctgctctcta-------gaatttgat-tataactgttcgatttgtaagttatcctttttatgttgaacagTTGCTTCGTCCAATTTACAAGCAAATTGCTGAAAATAGGAACGCTGAGATATTTTCAGCAAATACTCTCCTTGTTATTTTTGGAACAAGTCTTCTCACAG

upper sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 17
gtgagtttactgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactctaggctcagctggacatgggcttgtttctttgcttgcatgcatgtttcagttttttctccttgcagctgaatttaatctgcaactatgtaatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                      |  ||   |  |||    | |    || | |     |  |  |    |||||| || |   | | |||   | |||  ||||   ||||  || |   |   |||| | ||||| || || ||||||||  |||| |||||||| ||||| || || || ||||| |||||||||||||||||| |||||||||||||||||||||
-----------------------------------------------------------------------------------gataagtgatatcattttggggttcatttggaaggcattgcatgcttcaattgcagatgta--gagtatgc---tttgtgctgagt--tttctgttcttcttt--acagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCTAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG

upper sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
gtgagtttactgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactctaggctcagctggacatgggcttgtttctttgcttgcatgcatgtttcagttttttctcc-ttgcagctgaatttaatctgcaactatgtaatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                     || ||    |||    |    | | | ||||      ||  |   ||  |||||| || |   | | |||   | |||  ||||   || |  || |   |   |||| | ||||| || || ||||||||  |||| |||||||| ||||| || || || ||||| |||||||||||||||||| |||||||||||||||||||||
------------------------------------------------------------------------------------tgatatcattttggggttcacttggaaggcattgcatggtggtacttcaattgcagatgta--gagtatgc---tttgtgctgagt--ttcctgttcttcttt--acagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG

upper sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagtttactgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactctaggctcagctggacatgggcttgtttctttgcttgcatgcatgtttcagttttttctccttgcagctgaatttaatctgcaactatgtaatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                        ||||| |||  |       |      |   |  || |  | || ||| | || |   | ||||   |  | |  ||||    |||    || ||   || |||| | || ||||| || |||||||||||||| ||||| |  |||||||||||||| || || |||||||| || |||||| |||| || ||| | |||||||
---------------------------------------------------------------------------------------aatgggtttgcatgaacatataatgaaactctatagctaatgctgctt-ctgcggtgctgaatc-atagttttacaatgc---attgattttctggtacacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG

upper sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 9
gtgagttt-actgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactc---taggct-cagctggacatgggcttgtttcttt-----gcttgcatg--catgtttcagttttttctccttgcagctgaatttaatctgc--aactatg---taatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
|| ||| | | || |  | ||  || | ||      |   | |  || |   ||      | | |   |||  |   || |          ||||  | || | | |       | |||||||  ||| |        | | |   |   ||||  | |    |||  ||  ||    | |  |   |||    || ||   || |||| | || ||||| || |||||||||||||| ||||| |  |||||||||||||| || || |||||||                                 
gtaagtctcaatggttttctagtttctgttttgagactcatatccgaataagttaaacaacaaaagagagatccatataagtgatgagaaaacattagattttctatagaatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgctgaatcatagTTTTACAATGCATTGATTTTCTGGTACACACAGCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACAC---------------------------------

upper sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
gtgagtttactgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactctaggctcagctggacatgggcttgtttctttgcttgcatgcatgtttcagttttttctccttgcagctgaatttaatctgcaactatgtaatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                      |    | ||||| |    || | |    |||||||    ||   |  ||  |    | |  |  ||||| || || | | |    ||| ||| |  | |    ||| | ||| | || ||||| |||||||||||||||||||| ||||| ||||||||||| || |||||||| |||||||| || || || ||||| |||||||
--------------------------------------------------------------------------------------attgagacttgtgttacagcat-ctgatatgtttct-ccttcagttattata-tgaagtacagcctgcacct-tgcacttatttttttgcatctgctttt--gcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG

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|71449648|gb|DR830698.1|DR830698
EST:     CAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG                         TTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATA
genomic: CAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagtttac ... tatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATA
EST: gi|74240304|gb|DT648218.1|DT648218
EST:     CAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG                         TTGCTTCGGCCTATTTACAAGCAAATTG
genomic: CAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagtttac ... tatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTG

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: 53

GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagtttac ... tatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagtttac ... tatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagtttac ... tatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagtttac ... tatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgaatttaatctgcaactatgtaatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
      atttaat  putative branch site (score: 71)
     aatttaatct  TA-rich tract