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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggactgtatccagccctcgaagtgtgatatttctggagaaattataatactggtaaaccatgtggaccagcaatttttgtgacagcacagttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTGGTGGACGCCCGGCTTAACAAGAACTACAACGAAGTCGAGATGTTCCGTA

Basic information

species Zea mays
transcript GRMZM5G872442_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G872442_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g02040.1 (Oryza sativa), 3'ss of exon 6
ggactgtatccag-ccctcgaagtgtgatatttctggagaaattataatactggtaaaccatgtggaccagcaatttttgtgaca-gcacagttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTGGTGGACGCCCGGCTTAACAAGAACTACAACGAAGTCGAGATGTTCCGTA
  |    ||   | |     || | ||| |  ||||  |||||  |  |     | |  | |   ||   |    || ||| ||   |||| | | |||||||||||||||||||||||  | ||  ||||||| |||||||  ||||||||| | ||| || ||||  ||||||||| ||| ||||  || ||||| || |
atataaaatgtggactggtcaactatga-acatctgctgaaatcgtgttgtaaatcagtc-taaagaggggatccttgtgtaacttacacaatcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTGATTGACTCCAGGCTGGACAAGAACTTCAATGAAGCTGAAATGTTTCGAA
















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|26559092|gb|CA831327.1|CA831327
EST:     AGCCTGTCGACGCATCAAAGCCATTGGGTGACGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACGCAGGCGCTTGAGA
genomic: AGCCTGTCGACGCATCAAAGCCATTGGGTGACGAGAGCCTTGTTGAGTGGgtaagctata ... ttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGA
EST: gi|76289772|gb|DV029340.1|DV029340
EST:     AGCCTGTCGACGCATCAAAGCCATTGGGTGACGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
genomic: AGCCTGTCGACGCATCAAAGCCATTGGGTGACGAGAGCCTTGTTGAGTGGgtaagctata ... ttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
EST: gi|19770057|gb|BQ034778.1|BQ034778
EST:     CCTTGTTGAGTGG                         GCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
genomic: CCTTGTTGAGTGGgtaagctata ... ttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
EST: gi|37391450|gb|CF632968.1|CF632968
EST:     CGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
genomic: CGAGAGCCTTGTTGAGTGGgtaagctata ... ttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
EST: gi|71432382|gb|DR813432.1|DR813432
EST:     AGCCTGTCGACGCATCAAAGCCATTGGGTGACGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
genomic: AGCCTGTCGACGCATCAAAGCCATTGGGTGACGAGAGCCTTGTTGAGTGGgtaagctata ... ttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
EST: gi|87156672|gb|DY401461.1|DY401461
EST:     AGCCTGTCGACGCATCAAAGCCATTGGGTGACGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
genomic: AGCCTGTCGACGCATCAAAGCCATTGGGTGACGAGAGCCTTGTTGAGTGGgtaagctata ... ttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTG
EST: gi|37385210|gb|CF629731.1|CF629731
EST:     GCCTTGTTGAGTGG                         GCTAGGCCA-TGCTTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCT
genomic: GCCTTGTTGAGTGGgtaagctata ... ttatttgcagGCTAGGCCATTGC-TCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatactggtaaaccatgtggaccagcaatttttgtgacagcacagttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTGGTGGACGCCCGGCTTAACAAGAACTACAACGAAGTCGAGATGTTCCGTA
                          aatttttgt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggactgtatccagccctcgaagtgtgatatttctggagaaattataatactggtaaaccatgtggaccagcaatttttgtgacagcacagttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTGGTGGACGCCCGGCTTAACAAGAACTACAACGAAGTCGAGATGTTCCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- -ctgtatc
- - - - - - - - - - - - - - - - - - - - - - - -tactggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acagcac