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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatcttcatatcaggactaactttacatagctgtcatgataagttgatgcacctttagttcgcaaattctaagttactaatttgccaatgtgttttagGTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTTGTGGAACATTTCTTCCTTGTCAATCATCCTGATCATTATCTACAACACC

Basic information

species Zea mays
transcript GRMZM2G456000_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G456000_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g51630.2 (Oryza sativa), 3'ss of exon 3
------------aatatcttcatatcaggactaactttacatagctgtcatgataagttgatgcacctttagttcgcaaattctaagttactaatttgccaatgtgttttagGTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTTGTGGAACATTTCTTCCTTGTCAATCATCCTGATCATTATCTACAACACC
            |||   ||||||||   | | | |  |||          ||| |||| ||   | | | ||| |    ||  | |   || |  ||   || | |||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| ||||| |||||||||||||| |||||||||||||||||||||  |||||
gttgtagacgggaatggtttcatatctcaattgaataaacac---------gatgagttaatttccttctggttggtttgttgaatgcacctcaaatg---atttattttagGTTCTTGTGCGGAATATACCTCCAGATCCTGATGAATCAATTAGTGAGCTCGTGGAGCATTTCTTCCTTGTTAATCATCCTGATCATTATCTAAGACACC

upper sequence: GRMZM2G456000_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 4
aatatcttcatatcaggactaactttacatagctg-tcatgataagttgatgcacctttagttcgcaaattctaagttactaatttg-ccaatgtgttt-tagGTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTTGTGGAACATTTCTTCCTTGTCAATCATCCTGATCATTATCTACAACACC
   | |||| || |   |  ||  |     |     |  ||| ||     |  | |||  |||  |  || ||   |   | ||       |  | | |  |||| |||||  | ||| ||||||| ||||||||||||||  |||||||||| ||||||||||||||  | ||||||||||| ||||| |||||    || |
---accttcctacctttaaaaatatagaggaaaaacttttgacaataaactttatcttgtgtttccccatgcttgctccttcatgcaatttacatttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC

upper sequence: GRMZM2G456000_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G39320.1 (Glycine max), 3'ss of exon 4
aatatcttcatatcaggactaactttacatagctgtcatgat--aagttgatgcacctttagttcgcaaat-tctaagttactaatttgccaatgtgttttagGTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTTGTGGAACATTTCTTCCTTGTCAATCATCCTGATCATTATCTACAACACC
    |  |    | |    | ||   || ||  | | |  ||  |  |  |||     || | ||    || | |   ||| | |       ||   ||| |||| || ||  | || || ||||||||||||||||||||  | |||||||||||||| || || || || ||||| ||||| ||| | |||||    ||||
---gttatggactgaaaggttacaccacttacatattagcatttatatatatgagatattcgatcatgcatattttgcttattgaaaaaaatattattttcagGTGCTCGTTAGAAACATTCCACCAGATCCTGATGAATCTGTAAGTGAGCTTGTGGAGCACTTTTTTCTGGTCAACCATCCAGATAACTATCTTACTCACC

upper sequence: GRMZM2G456000_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 3
---aatatcttcatatcaggactaactttacatagctgtcatgataagttgatgcacctttagttcgcaaattctaagttactaatttgccaatgtgttttagGTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTTGTGGAACATTTCTTCCTTGTCAATCATCCTGATCATTATCTACAACACC
     |   || || |    || |  |||    |  |||   | | | |  |||     |      ||| ||| |   |||   |   |  | | | ||| |||| || ||  | || || ||||||||||||||||| ||  |||||||||||||||| || || || || ||||||||||| ||| | |||||    ||||
tttttttctttaatcttttaacaagttttgggaaattgtagcgttta-tatatgtgagatattcgtgcatattttgc-ttatagaaaagatattat-tttcagGTGCTCGTTAGAAACATTCCACCAGATCCTGATGAGTCTGTCAGTGAGCTTGTGGAGCACTTTTTTCTGGTCAATCATCCAGATAACTATCTTTCTCACC

upper sequence: GRMZM2G456000_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G15430.1 (Arabidopsis thaliana), 3'ss of exon 4
aatatcttcatatcaggactaactttacatagctgtcatgataagttgatgcacctttagttcgcaaattctaagttactaatttgccaatgtgttttagGTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTTGTGGAACATTTCTTCCTTGTCAATCATCCTGATCATTATCTACAACACC
    |  | | |    | ||| || |  ||   | | |   ||   |||   | |  |    |   |  |  || ||  | |  || |  |   | |||||| || ||  | || || ||  |||||||| ||||||||||  |||| ||||| ||||||||||||   ||||||||||| ||||| |||||      ||
---gtaatgaaactttg-ctacctgttgatgttttttactcta---tgacaaaaccatttccccatagctgaaacttgttgaactgtc--ttcatcttagGTACTGGTAAGAAACATTCCTGCAGATCCTCATGAATCAATATGTGAACTTGTTGAACATTTCTTCAAAGTCAATCATCCAGATCACTATCTCACTTTCC

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|78105551|gb|DV523969.1|DV523969
EST:     TGAGGCTGCGCTTTCTAGCTTCAGAGAAACGCCGACCAGATCAGTTCACT                         GTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTT
genomic: TGAGGCTGCGCTTTCTAGCTTCAGAGAAACGCCGACCAGATCAGTTCACTgtatgttctt ... tgtgttttagGTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgcacctttagttcgcaaattctaagttactaatttgccaatgtgttttagGTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTTGTGGAACATTTCTTCCTTGTCAATCATCCTGATCATTATCTACAACACC
                               tactaat  putative branch site (score: 1)
                          taagttactaattt  TA-rich tract