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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgaccctttccctgatccgcgcaagcgggagcacatgcaccgggcataattacattgtggtttcttatagtttctgttgacctacctgattcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGTCTATTGCACCAACCTGTCTATCGGAATCAGAATTTTAA

Basic information

species Zea mays
transcript GRMZM2G137348_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137348_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g06280.1 (Oryza sativa), 3'ss of exon 6
-cgaccctttccctgatccgcgcaagcgggagcacatgcaccgggcataattacattgtggtttcttatagtttctgttg-acctacctgattcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGTCTATTGCACCAACCTGTCTATCGGAATCAGAATTTTAA
   |   |      ||    |  |  |       | | | |   |  ||  |   ||  | | | |||    || ||||| || |   | |||| |||||||||||||||||||| || || ||||||||||||||||||||||||||||||||||||||||| || ||||| || |||||||| || ||||| ||||||||
gtaaatttggaaaagaaaatctaattcttttattctttctcaaagtttacctt--tttagatcttttactagttttgttgtacttttttcattcatgagcagGTAGTGGCAAGACATATACGATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGCCTTTTGCATCAGCCTGTCTACCGTAATCAAAATTTTAA

upper sequence: GRMZM2G137348_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G04960.1 (Glycine max), 3'ss of exon 7
cgaccctttccctgatccgcgcaa-gcgggagcacatgcaccgggcataattacattgtggtttcttatagtttctgttgacctacctgattcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGTCTATTGCACCAACCTGTCTATCGGAATCAGAATTTTAA
  |    ||   | ||    |       |  |  | ||  ||    | | | ||           | |   || | | ||       || || |    |||| |||||||| || ||||||||||||||||| || || ||||||||| ||||| | ||||| |  ||||| || || || || ||||||||||  |||||
atataagtttgttcatttatgttccattgctgtgcttgatcctcagacagtcactccacttgcattcactattac-gatgctaataatgctttgctttcagGAAGTGGCAAAACATACACAATGCAACCTTTACCACTCAGAGCTGCAGAAGACCTTGTTCGACAGTTGCATCAGCCAGTTTACCGGAATCAGAGATTTAA

upper sequence: GRMZM2G137348_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G15900.1 (Glycine max), 3'ss of exon 7
cgaccctttccctgatccgcgcaa-gcgggagcacatgcaccgggcataattacattgtggtttcttatagtttctgttgacctacctgattcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGTCTATTGCACCAACCTGTCTATCGGAATCAGAATTTTAA
  |    ||   | || |  |       |  |  | ||  ||    | |   ||           | ||  ||  || ||       || || |    |||| |||||||| || ||||||||||||||||| || || ||||||||| ||||| | ||||| |  ||||| || || || || ||| ||||||  |||||
atataagtttgttcattcatgttccattgctgtgcttgatcctcagacagccactccacttgcattcattatta-tgatgctaattatgctttgctttcagGAAGTGGCAAAACATACACAATGCAACCTTTACCACTCAGAGCTGCAGAAGACCTTGTTCGACAGTTGCATCAGCCAGTTTACCGGGATCAGAGATTTAA

upper sequence: GRMZM2G137348_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G03020.1 (Glycine max), 3'ss of exon 7
cgaccctttccctgatccgcgcaagcgggagcacatgcaccgggcataattacattgtggtttcttatagtttctgttgacctacc--tgattcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGTCTATTGCACCAACCTGTCTATCGGAATCAGAATTTTAA
  |  |||   |  |   |  | |  |  |   | |   ||    ||  | ||    |   ||    |  ||  |||    |||    || ||      |||| |||||||| || |||||||||||||| ||||| || ||||||||| ||||| | ||| | | |||||| | ||| || ||||| |||||||  |||||
--aagcttgttcatacatgttccactgctactcctttatccccatattttcactacattactttcattcattattgtgacgctaataatgttttactttcagGAAGTGGCAAAACATACACAATGCAACCGTTGCCGCTCAGAGCTGCAGAAGACCTTGTTAGACAATTGCATCGACCAGTATATCGAAATCAGAGATTTAA

upper sequence: GRMZM2G137348_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G37630.2 (Glycine max), 3'ss of exon 7
cgaccctttccctgatccgcgcaagcgggagcacatgcaccgggcataattacattgtggtttcttatagtttctgttgacctacc--tgattcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGTCTATTGCACCAACCTGTCTATCGGAATCAGAATTTTAA
  | | | | | | ||  |  | |  |  |   | |   ||    ||  | ||    |   ||    | |||  |||    |||    || ||       ||| |||||||| || |||||||||||||| ||||| || ||||||||| ||||| | ||| | |  ||||| | ||| || ||||| |||||||  |||||
aaagcttgttcgtaat--gttccacagctactcctttatccccatattttcactccatcactttcatttgttattgtgatgctaatagtgttttactttaagGAAGTGGCAAAACATACACAATGCAACCATTGCCGCTCAGAGCTGCAGAAGACCTTGTTAGACAGTTGCATCGACCAGTATATCGAAATCAGAGATTTAA

upper sequence: GRMZM2G137348_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0020g01200.t01 (Vitis vinifera), 3'ss of exon 6
cgaccctttccctgatccgcgcaag-cgggagcacatgcaccgggcataattacattgtggtttcttatagtttctgttgacctac--ctgattcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGTCTATTGCACCAACCTGTCTATCGGAATCAGAATTTTAA
  |  |     || |||       | | |  ||   | |    ||  |||  | |   ||  | || ||        ||||  |||  || |||      |||||||||| |||||||  || ||||||||||| ||||| ||||||||  ||||  | ||| |  | ||||| || ||    |||||||||||||  |||||
-tattcaccttcttatctttttgtgtctgctgcctgttcctgaggtgtaac-agaccctgact-ctgatgtggataattgaattacaactaatttaatttcagGTAGTGGTAAGACGTTTACCATGCAACCTTTACCTCTCAGAGCTGCTGAAGATCTTGTTAGATTGTTGCATCAGCCAACTTATCGGAATCAGAGGTTTAA

upper sequence: GRMZM2G137348_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S293_5V6.1 (Physcomitrella patens), 3'ss of exon 6
cgaccctttccct-gatccgcgcaagcgggagcacatgcaccgggcataattacattgtggtttcttatagtttct-gttgac-ctacctgattcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGTCTATTGCACCAACCTGTCTATCGGAATCAGAATTTTAA
     ||| |  | || | |   ||  |     ||   |  |     |||||| |||     ||  | ||    ||     |  | | |||    ||  | ||| ||||| ||||||||||| ||||| ||||||||||| ||||||     ||||||  |     |  |||| || ||    || || ||||||   ||  |
tattacttgcttttgagctggagaaatgttgttacgctcttctt-tgtaatta-attactcatttatgtacccacttaccaatgccaactggcg-gttggtagGAAGTGGAAAGACGTACACGATGCAGCCTTTGCCTCTAAGAGCTTGTGGAGACATTATGGCCATCATGCAGCAGCCGAATTACCGCAATCAGGGCTTCCA

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|60343423|gb|DN210396.1|DN210396
EST:     AATTATATTTCAGAGAACGAAAGCAACATGTTTTGCTTATGGCCAAACAG                         GTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAG
genomic: AATTATATTTCAGAGAACGAAAGCAACATGTTTTGCTTATGGCCAAACAGgtttgctcgt ... tcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataattacattgtggtttcttatagtttctgttgacctacctgattcgtgagcagGTAGTGGCAAGACGTACACAATGCAACCTTTGCCTCTGAGAGCTGCACAAGACATGGTTCGTCTATTGCACCAACCTGTCTATCGGAATCAGAATTTTAA
               tttcttata  TA-rich tract