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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccagagcacacgccgccattattggcccccctctgctccgctcgttccgtttcgtttccactagccgtccaataatgttgccctgccatcgatggaccgagcagCATGTTTGGGCCGGTGCAGGATGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACGCCGAGACGGTGAAGGCCATCCTG

Basic information

species Zea mays
transcript GRMZM2G346113_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G346113_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g03220.1 (Oryza sativa), 3'ss of exon 2
---gtacccagagcac-acgccgccattattggcccccctctgctccgc-tcgttccgtttcgt--ttccacta--gccgtccaataatgttgccctgccatcgatggac-cgagcagCATGTTTGGGCCGGTGCAGGATGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACGCCGAGACGGTGAAGGCCATCCTG
     ||      ||| |    |||  |||||      ||    ||    | |   | |||| |  ||  |  |  ||  ||   |   | |    ||   |   |||   | | |||||||| ||||  |||||| |||||||| ||||| |||||| ||||||||||||| || || ||||||||||  |||    |||| ||||||   || || 
gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgttgtgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGCGCATGTTTGGTTTTGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT

upper sequence: GRMZM2G346113_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g02970.1 (Oryza sativa), 3'ss of exon 2
---gtacccagagcac-acgccgccattattggcccccctctgctccgc-tcgttccgtttcgt--ttccacta--gccgtccaataatg-ttgccc-tgccatcgatggaccgagcagCATGTTTGGGCCGGTGCAGGATGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACGCCGAGACGGTGAAGGCCATCCTG
     ||      ||| |    |||  |||||      ||    ||    | |   | |||| |  ||  |  |  ||  ||   |   | |||    || |||    ||||  | |||||||| ||||  |||||| |||||||| ||||| |||||| ||||| ||||||| || |||||||||||||  |||    |||| ||||||   || || 
gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggac-aaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT

upper sequence: GRMZM2G346113_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G63450.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacccagagcacacgccgccattattggcccccctctgctccgctcgttccgt-ttcgtttccactagccgtccaataatgttgccctgccatcgatggaccgagcagCATGTTTGGGCCGGTGCAGGATGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACGCCGAGACGGTGAAGGCCATCCTG
                                     |  | | || |||  |    | ||    ||    ||   ||  |||   | |   | | ||||   | |||| | ||||||||| || ||||| ||| | || || |||||||||||| | ||||| |||||||| |||||| ||||| | ||||| ||||||  ||| |||
------------------------------------gtattactcttgtttggaacccattcattcttcttgttggatgttgtctacttaa-agcaatgg-tggtgcagTACGTTTGGGCCAGTTCAGGACGTGAGGATACCTTACCAGCAGAAGAGGATGTTTGGGTTCGTGACCTTCATGTACCCAGAGACTGTGAAGAGCATTCTG

upper sequence: GRMZM2G346113_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
gtacccagagcacacgccgc-cattattggcccccctctgctccgctcgttccgtttcgtttccactagccgtccaataatgttgccctgccatcgatggaccgagcagCATGTTTGGGCCGGTGCAGGATGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACGCCGAGACGGTGAAGGCCATCCTG
         | |   ||  |   ||  | |      ||| |       | | ||| | ||      |||    || |    |||| | ||    |  | ||      || || |||||||| || || |||||| | || || |||||||||||| | |||||||| |||||||| ||||| ||| ||||||| ||||||  |||  | 
---------gtaattgctacgtgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaaccta----gttggcttgtgtgcttttga------agTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA

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|26457315|gb|CA828898.1|CA828898
EST:     TTCCCGGCCGACTCCACCTTCAGCGAGGAGGACGTGTCCAACTACTTCAG                         CATGTTTGGGCCGGTGCAGGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCCGACTCCACCTTCAGCGAGGAGGACGTGTCCAACTACTTCAGgtacccagag ... gaccgagcagCATGTTTGGGCCGGTGCAGGATGTGCGCATCCCGTACCAGCAGAAGCGCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtttccactagccgtccaataatgttgccctgccatcgatggaccgagcagCATGTTTGGGCCGGTGCAGGATGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACGCCGAGACGGTGAAGGCCATCCTG
                     aataatgtt  TA-rich tract