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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_T02
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttaatttgaaatgatctagtgctaatttttttgtttgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
                      tgctaat  putative branch site (score: 2)
                         taatttttttgtttgt  TA-rich tract