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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accaggttaaatttaacaatgatattgttttctttagtaccctgtttattgagaaattcccatcttgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT

Basic information

species Zea mays
transcript GRMZM2G094497_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 5
accaggttaaatttaacaatgatattgttttctttagtaccctgtttattgagaaattcccatcttgtttgattatacagtcattgtg----tttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
    |  |||  |  |   |  | | ||||   |   | || |||||     | |   |  |  | |    |||    | |   ||||    ||  || || ||||  |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| |||||||| || || ||||| || |||||||
---tgaataatctataagtttttgtagtttatatcttttccttgtttgc-atgtagcactgaagtagcggcattgcttaatatgtgtggtaattctttctatagGTCCTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACT

upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 5
-----accaggttaaatttaacaatgatattgtt-ttctttagtaccctgtttattgagaaattcccatcttgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
         |  |   ||| ||| || || | ||  | | | | |  |  ||||||    |  |   | |||  |   || | |  || || ||||| |   |||||| || ||||||||||||||||| || |||||||| ||||| |||||||| ||||||||||| ||||| ||||| || || || || || || || ||| 
tttttctttgaatttcttttaca-tgctacttttactgtattggaatcaatttattc--caccttttaacttcctc--ttttcctctctttttgtttgtcc-acagGTGTTAAAAACTCCTGTCTCACTAGACATGCTTGGACGCATATTTAATGGCTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 5
-----accaggttaaatttaacaatgata--ttgttttctttagtaccctgtttattgagaaattcccatcttgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT-
     |     |    ||| |   ||||   ||| |||  || | | |  |||||       | |||||| ||      ||    | | ||||| |||  || |||||| || |||||||| || ||| | || |||||||| ||||| || ||||||||||||||||| ||||| ||||| || || || || || || || |||| 
tgattattgaatcctttttcattttgattctttgattttgtttgaatca-gtttaactgttgactcccatttt------ttccttaattattgt-ttttgttcacaggTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATTTTACCTGAGGCTTACTT

upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
---accaggttaaatttaacaatgatattgttttctttagt---accctgtttattgagaaattcccatcttgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
   |  |    |  |||  || |   |||||||  |||  |   |  | |||||       | |||||| || |||       || | ||||| |||  || |||||| || |||||||| || ||| | || |||||||| ||||| || ||||||||||||||||| ||||| ||||| || || ||||| ||||| || ||||
ttgattattgaatctttttcattttgattgtttgatttgctttgattcagtttaactgttgactcccatttttttt-----ctcaattattgt-ttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT

upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
-accaggttaaatttaacaatgatattgttttcttta----gtaccctgtttattgagaaattcccatcttgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
       || |||||       || ||  |||  ||     | |  | |||||||    |  |     |||  |   || | |  || || ||||| |   |||||| || ||||||||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||| ||||| || || || || || || || ||| 
tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattc--caccttttgacttcctc--ttttcctctctttttgtttgtcc-acagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 5
-------accaggttaaatttaacaatgatattgttttctttag---taccctgtttattgagaaattccca--tcttgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
       ||||    ||||    |     |   |  ||    ||   |       | ||||    ||| |    || ||  |  || |  |  |  | ||| |||||  |||||||||||||| ||||| ||| | || |||||||||||||| ||||| ||||| ||||| || ||||| |||||||| || ||  |||| ||||| ||| 
gtaatttaccataa-aaatccttcgtccctccagcatttcgcagatttgttgaaatgattggttgatttctgcttcctgcattttttttaaaccggtttgtgtcttt--cagGTTTTGAAAACACCTGTATCATTGGACATGCTTGGGCGCATATTTAACGGTTCAGGAAAGCCGATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACC

upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
accaggttaaatttaacaatgatattgttt-tctttagtaccctgtttattgagaaattcccatcttgtttgattatacagtcattg-tgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
                          |||| | |||  ||||  |||  || |   ||     |||    |      ||| |      ||||| ||  | ||||||||||||||||||| ||  | ||||||||||| ||||| || |||||||| || || || |||||||| || || || |||||||| || || ||||
--------------------------gtttgtttttgctaccaagtt--ttaaagtatcagtgtctataatatactcacattttccaatgttttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT

upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
accaggttaaatttaacaatgatattgttttctttagtaccctgttta--ttgagaaattcccatct-----tgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
     || ||   |  |  ||||  || | ||| ||||| |   || |  |  |    || |  |||     | ||| ||| |       |  |     || |||||||||||||||||||||||||| | |||||||||||||| || ||||||||||| || ||||| ||||| ||||| || || |||||||| || || ||||
-----gtcaagcctttctgtgat--tgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT

upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 5
accaggttaaatttaacaatgatattgttttctttagtaccctgtttattgagaaattcccatcttgtt-tgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
 |    |  |    | |  |  | ||   || |    | | | |||| |    | |||       ||   || || |   ||       ||| || | |||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||||||||| ||  |||| || || ||| 
-ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggcaatgaaatgtttgtctggttgaatattttgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC

upper sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 5
accaggttaaatttaacaatgatattgttttctttagt--accctgtttattgagaaattcccatcttgtttgattatacagtcattgt--gtttcttttac-----agGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
         | | |   ||||||||| | || ||   |  | |  | ||     || ||     |  |  | ||||||  |      ||  |||  | ||       ||||  ||||||| || |||||  | || ||||| || || ||||| ||||||||||| |||||||||||||| ||||| || ||  |  | ||||| ||  
---------attgtccgaatgatattctatttttctatggatcgcggttgggccgacatgtgtttactactcgattatcgacctgcagttggttcttgttgtggtttagGTGCTGAAAACACCAGTCTCGTTAGACATGCTGGGACGTATTTTCAATGGTTCTGGCAAACCTATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATC

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|32910787|gb|CF015599.1|CF015599
EST:     GACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT
genomic: GACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtacttcatc ... tcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32929168|gb|CF033980.1|CF033980
EST:     AACTTCTGGAATAGACAACAAATACACANCCGTGCAG-TTACAGGCNGAG                         GTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGG
genomic: AACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGC-GAGgtacttcatc ... tcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGG
EST: gi|32838409|gb|CD978087.1|CD978087
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtacttcatc ... tcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32850751|gb|CD990432.1|CD990432
EST:     TGCAGTTTACAGGCGAG                         GTTTTGANAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT
genomic: TGCAGTTTACAGGCGAGgtacttcatc ... tcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|194716810|gb|FK933969.1|FK933969
EST:     GAACTTCTGGAATAGACAACAAATACACAACTGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtacttcatc ... tcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|33102277|gb|CF062237.1|CF062237
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtacttcatc ... tcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgagaaattcccatcttgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT
                     gtttgat  putative branch site (score: 5)
                                         tgtttctttt  putative PPT
                      tttgattata  TA-rich tract