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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttgccgagtctttcagctacagctcgcctgtgattggacatattgggtggcgttaattaacctgctccaatttctgttagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTG

Basic information

species Zea mays
transcript GRMZM2G010044_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
gtaccttgccgagtctttcagctacagctcgcctgtgattggacatattgggtggcgttaattaacctgctccaatttctgt-tagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTG
|||| |   | |||   |  ||||  ||  |  | || | ||    || ||   |     |||||||||||||||||  ||| ||||||||| | || ||||||||||||||||||||||||||||| ||||| || |||||||||||||| |||||||||||||| ||||||||| |||||||||
gtactt---ccagtgaatgtgctaatgcaggaatctggt-ggtttcataggacag----gattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG

upper sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 5
-------gtaccttgccgagtcttt---cagctacagc------tcgcctgtg-attggacata---ttgggtggcg-ttaattaacctgctccaatttctgttagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTG
        ||  ||  | ||| |||       || ||       | |    |   || |||| |   |||| |   | ||   |||  |    |  || |    |||||||||| || ||||||||||| || || | ||||||||| ||||| || ||||| || || || || || |||||||| || |||||| |||| ||| 
ggttcgcttagtttaaccagtttttattttattatagtgaagtattgttcatttgtttgacagaagtttggttcctgctttgctaatttctctctgttacctgcaGGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGCCAATTTGCTACAGGGATTGGTAATACTGATGCTGGCTTTGTGCTGGGAACT-

upper sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 5
------gtaccttgccgagtctttca--gctacagctcgcctgtgattggacatattgggtggcgttaattaacctgct-ccaatttctgt--------tagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTG
       ||  ||  | ||| |||      || ||     |  || |      | |         ||  ||   |   | | ||||||| |         |||||||||| || ||||||||||| || || | ||||||||| |||||||| ||||| || || || || || |||||||| || |||||| |||| ||||
gtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGTAATACTGATGCCGGCTTTGTGCTGGGAACTG

upper sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
----gtaccttgccgagtctttcagctacagctcgcctgtgattggacata---ttgggtggcgttaattaacctgctccaatttctgt----tagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTG
      | ||     | |   |  | |   |||  | |||||||| | ||    |||  ||    |  |  |  || |    ||| | |    |||||| | || || || || || || || || | ||||||||| |||||||| ||||| || || || |||||||||||||||||||||||||| |||||||
gtaaagatctctttcactggatatgat-tggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG

upper sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------gtaccttgccgagtctttcagctacagctcgc-------ctgtgattggacatattgggtggcgttaattaacctg-ctccaatttctgttagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTG
                                                   ||  || |  ||    | ||||  |  ||  |       | ||  |||||  | | |   |      |  | | || || ||||    || |||||||||| ||||| ||||| || || |||||||||||||| ||||||||||||||||| || ||||| |||||||||||||| ||| |  ||||||| |
gtatttgttacggaagttttcgttactgtcgaatatgccgtagtgcataatgttgctcgttgacatatgcagccccgtctaccacatttacagtttttggatttttcgcaagttaaatacgatcgtggcttcaatgggcgt-agGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAGTTTGCAACAGGGATCGGTAACACTGATGCAGGCTTTATTATGGGCACCG

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|71772889|gb|DR970812.1|DR970812
EST:     GCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG                         GTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAG
genomic: GCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAGgtaccttgcc ... tttctgttagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAG
EST: gi|76012112|gb|DT939282.1|DT939282
EST:     GCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG                         GTTCTCTTGGGCACTGATTCTCATACATGCCATGCTGGAGCTTTTGGTCAG
genomic: GCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAGgtaccttgcc ... tttctgttagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAG
EST: gi|31355882|gb|CD440239.1|CD440239
EST:     GCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG                         GTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAG
genomic: GCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAGgtaccttgcc ... tttctgttagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAG
EST: gi|31354069|gb|CD438426.1|CD438426
EST:     GCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG                         GTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAG
genomic: GCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAGgtaccttgcc ... tttctgttagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgtgattggacatattgggtggcgttaattaacctgctccaatttctgttagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTG
                             aattaac  putative branch site (score: 2)
                                             tttctgtt  putative PPT
                           ttaattaa  TA-rich tract