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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGAATATACTTGATGCTCGGAATTCAGAAATGTTCGAGAGCCGTTTCCTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggttttataccatcggctgatgactgatgcacactttgtccaagtagttttagcgaaccatgttccttctgaccgaattgcttgctctattttcctttggcag

Basic information

species Zea mays
transcript GRMZM2G474236_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G474236_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g31460.1 (Oryza sativa), 5'ss of exon 16
CCTGGAATATACTTGATGCTCGGAATTCAGAAATGTTCGAGAGCCGTTTCCTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggttttatacc-atcggctgatgactgatgcacactttgtccaagtagttttagcgaaccatgttccttctg-accgaattgcttgctctattttcctttggcag
||||||||| | | || || |||| ||| | ||| ||||| || ||||||   |||||||||||||| ||||| ||||||||||| |||||||||||  |||  |||  ||| | ||| |||| |      |||  | |||   |      |||| || ||| |||||   | ||      |  |                       
CCTGGAATACAATAGACGCCCGGAGTTCTGTAATTTTCGACAGTCGTTTCTATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaatatctatctgctggtagtgattgctgaattttctccc----ttttggctaacaatgttttatatgcgtttgacag-----------------------
















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|211120309|gb|FL433022.1|FL433022
EST:     TTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCTCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|26558437|gb|CA830672.1|CA830672
EST:     TTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCTCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|87155597|gb|DY400386.1|DY400386
EST:     TTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCTCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|32863285|gb|CF002967.1|CF002967
EST:     TTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCTCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|76926868|gb|DV171024.1|DV171024
EST:     CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTTTTCGCGTAAGAGATTCCCATTTTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|71766468|gb|DR964405.1|DR964405
EST:     CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGAT-CCCATTCTAATC-AAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|76919531|gb|DV167764.1|DV167764
EST:     CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTTTACGCGTAAGAGATTCCCATTTTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|4630556|gb|AI621430.1|AI621430
EST:     CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|12972387|gb|BG267956.1|BG267956
EST:     AGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
genomic: AGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|83279043|gb|DV943051.1|DV943051
EST:     CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|76291468|gb|DV031036.1|DV031036
EST:     CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|32935691|gb|CF040503.1|CF040503
EST:     TTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCTCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|18168893|gb|BM338733.1|BM338733
EST:     CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|32936388|gb|CF041207.1|CF041207
EST:     TTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCTCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|22545635|gb|BU097994.1|BU097994
EST:     TTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCTCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|71421571|gb|DR805500.1|DR805500
EST:     CTGAGGAAAACATTTCCAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTTTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|166516103|gb|EG166193.1|EG166193
EST:     AAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCTCATTCTAATCCAAGGTTTCAGAT
genomic: AAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
EST: gi|18168382|gb|BM338222.1|BM338222
EST:     CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAG                         GTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT
genomic: CTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggtttta ... cctttggcagGTTTAGGTTTCTACGCGTAAGAGATTCCCATTCTAATCCAAGGTTTCAGAT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGAATATACTTGATGCTCGGAATTCAGAAATGTTCGAGAGCCGTTTCCTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggttttataccatcggctgatgactgatgcacactttgtccaagtagttttagcgaaccatgttccttctgaccgaattgcttgctctattttcctttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA