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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtttgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG

Basic information

species Zea mays
transcript GRMZM5G846339_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 7
gtgagtttcatttgtgctctagtg-tactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtttgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
  |  |   | || ||||||  || || |||       |||  |||| |||||  || ||| |  |   ||  |||   ||| |||||| |  | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| || ||||| ||||| |||
--gtctgctactt-tgctctgatgctattgtcattctctcaggtgctcaattttgaaggatatcttctaaagattt--atttatgcacatacatgtagGTGGTATGCCAAAAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATCTGGGATGAGGACCTTGGGGTGGAGCATTTCAATGCGGAG

upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------------------gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatct-agtgctaatttt---tttgtttgtgcacacaactct--agGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
                                                                              |||| |  |||||   || | |  | ||      |  | |      | |   |  |||| || | ||||  | |    |||  | || |  |    | |  ||||||||||| || |||||  |||| |||||||| ||  |||||||||| || || || ||||||||||| || ||||| || ||||| || |||||||| 
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctattttttggtga-tcacattta-actttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgcttttatgcaatttcctcgtacttaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC

upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------------------gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatct-agtgcta-atttttttgtttgtgcacacaactct-----------------agGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
                                                                              |||| |  |||||   || | |  | ||      |  | |      | |   |  |||| || | ||||| | |  |||| || |  |||    |||                 ||||||||||| || |||||  |||| |||||||| ||  |||||||||| || || || ||||||||||| || ||||| || ||||| || |||||||| 
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtga-tcacattta-actttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC

upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtttgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
          || ||  ||| ||    |    |   || | |   ||  |     ||| | |  | | || || | |  | ||     ||      ||||||| || ||||| ||  ||||||||||| ||||| ||||||||||||||||||| || |||||||| || ||||| || || ||||| ||||| || 
---------gttagtcatctggtcatttaccggttattaagtatgtttgtcgagtatgtttttat-cgaaattctctactggttttggca------gGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT

upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
---gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtttgtgc-acacaactct---agGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
      | | | |  |||     ||     | | | |   |   |    || |    ||   |    | | || |  |    ||| ||     | || |   ||||||||||| ||||||||  ||||||||||| ||||  ||||||||||||| ||||| || |||||||| || ||||| || || || || |||||||| 
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT

upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
---gtga-gtttcatttgtgctctagt--gtactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtttgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
   | ||     ||||  ||    ||     ||| ||     | ||  |  |||||      ||  |||||    |||  |   ||       |    |  ||||||||||| || || ||| ||||||||||| |||| || |||||||| || || || || |||||||| ||||| |  ||  | || || |||| ||||
ggagagacacggcattattggctaagctgaaactttttctgctgcagatagttaatactttttgtcctagtttatattcatagattcccatgta---ttgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG

upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 7
gtgagtttcatttgtgctctagtgtactgttcgcagttcaatt--gcttaatttgaaatgatctagtgct--aatttttttgtttgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
     ||  |     | ||      |   |||   | |   ||    || ||||    || | | |   |   |||| ||  ||  ||    |   | |||||||||||||||| | ||  |||| || ||| | |||||  | ||||||||||| ||||||||||||||||| ||||   |    ||||||||| |  ||
tctgattagacacccgatccgaca-ataattcctggcttgtttttattttattttttttgttttcggaatcggatttattgattattgtttgctgttatagGTGGTATGCCAAGCGGTTTTTGCACCCCGATGTAGTGGCGCCGTATGAGTACATCTTCATTTGGGATGAGGATCTTGATTTGAGGCATTTTAATCCTAAG

upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtt-------tgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
   |      |||||   || |||     ||| || |   | | | |   | |   || |||  ||   |  || | |||       | |     ||| |  |||||||||| |||| ||||  ||||||||||| | ||||||   ||||| || || ||||||||||||||||| ||||   |    ||||| |||||   |
---atgcctgtttgt-tacttgtggtggattctcaatctgactacatttctggctctgctctgttgtcgaagttgtagttaactgattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG

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|32927854|gb|CF032666.1|CF032666
EST:     GAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATG                         GTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTA
genomic: GAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATGgtgagtttca ... acaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTA
EST: gi|44682283|gb|CK787331.1|CK787331
EST:     GAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATG                         GTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTA
genomic: GAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATGgtgagtttca ... acaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTA
EST: gi|148950258|gb|EC895810.2|EC895810
EST:     GAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATG                         GTGGTATGCCAAGAGATTCCTGCATCCTG
genomic: GAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATGgtgagtttca ... acaactctagGTGGTATGCCAAGAGATTCCTGCATCCTG

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: 60

CTATTCTGTTATTCCACTATGATGGCCGGGTGAGTGAGTGGGATGAATTTGAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATGgtgagtttca ... acaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

CTATTCTGTTATTCCACTATGATGGCCGGGTGAGTGAGTGGGATGAATTTGAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATGgtgagtttca ... acaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

CTATTCTGTTATTCCACTATGATGGCCGGGTGAGTGAGTGGGATGAATTTGAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATGgtgagtttca ... acaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 270

CTATTCTGTTATTCCACTATGATGGCCGGGTGAGTGAGTGGGATGAATTTGAGTGGTCCCAGCGAGCTATCCATATTAGTGTCAGGAAACAAACTAAATGgtgagtttca ... acaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttaatttgaaatgatctagtgctaatttttttgtttgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
                      tgctaat  putative branch site (score: 270)
                         taatttttttgtttgt  TA-rich tract