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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttatggactaaactttagtcccctaactaaactttagtccttagactaaagaaaccaaacatgaccttattctcttgacgcttttatattcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGGGCATGAGAGGCCAAAGACCAAAGAGGCAAAGACTGGTGCTAACCGTGGA

Basic information

species Zea mays
transcript GRMZM5G845755_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------------------------atgttatggactaaactttagtcccctaactaaactttagt--ccttagactaaagaaaccaaacatgacc-ttattctcttg-acgcttttatattcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGGGCATGAGAGGCCAAAGA-CCAAAGAGGCAAAGACTGGTG-CTAACCGTGGA
                                                                       |  | |||   |    |||       |  ||   | ||| |   ||  |||    ||        |  |     || | |||  |     ||  ||  |||||| ||||||||||||| |  |||||||||||||| |||||||| ||| | || |||  | || | ||||| |   |        |||||  |  || | |    
gtaagtaacttgttctgcacttcctttgatttccttttttctatgcaaaatatgcgttttactagtgtacaacatcatgatattttttttgcgattgttcctgggcattattggtctctgacctttgatttggtgtaccattgccatgcacttatataacattggatgattgcagGCACACCCATACTTTCTCCAAGTGAGGGCTGCGGAGAACAGTAGGCCTCGTGCACAATAGACAAAAGAACGGGACTATTGCTGACTGTCGATTAGCAGCA--
















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|6465600|gb|AW191195.1|AW191195
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|32846294|gb|CD985975.1|CD985975
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|194717129|gb|FK934282.1|FK934282
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|29945847|gb|CB815850.1|CB815850
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|60350778|gb|DN217751.1|DN217751
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|94476026|gb|EB704984.1|EB704984
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCACCAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|61117730|gb|DN558691.1|DN558691
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|60354727|gb|DN221700.1|DN221700
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|32849734|gb|CD989415.1|CD989415
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|4609748|gb|AI600587.1|AI600587
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|61117733|gb|DN558694.1|DN558694
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCTTACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|61117731|gb|DN558692.1|DN558692
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|61117732|gb|DN558693.1|DN558693
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCTTACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
EST: gi|148990947|gb|EE032376.2|EE032376
EST:     AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG                         ACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG
genomic: AGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATGgtaagtttcc ... attcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactaaagaaaccaaacatgaccttattctcttgacgcttttatattcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGGGCATGAGAGGCCAAAGACCAAAGAGGCAAAGACTGGTGCTAACCGTGGA
                                            tattctt  CT-rich tract
                                       ttttatattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttatggactaaactttagtcccctaactaaactttagtccttagactaaagaaaccaaacatgaccttattctcttgacgcttttatattcttgcagACACACCCATACTTCCAACAAGTGAGGGCTGCAGAGAACAGCAGGACGCGGGCATGAGAGGCCAAAGACCAAAGAGGCAAAGACTGGTGCTAACCGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG