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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatccttccatcagtgtcatttttctttgcaagttcatacctgttgaacctgtagccactaaatcagatatttgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT

Basic information

species Zea mays
transcript GRMZM2G447433_T08
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G447433_T08 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g27030.2 (Oryza sativa), 3'ss of exon 4
------------gtaaatccttccatcagtgtcatttttctttg-caagttcatacctgttgaacctgtagccactaaatcag-atatttgttatc-cagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT
             |    || |  || |     ||| | |     |||| | |      || | | | |    | |||   |  || |||||| |   ||||||| |||||| | ||    ||||| |||||||||||||||| ||||||||||||||||||  | ||||| ||||||||||||||||||||| 
aaagaattattttttgtgccatagattaagcaaattgtacagaaacaaggtaaacatcctttaccttattaaaagtaatcaattatttttgtttttgtagAATTTCAATAATGTCACTGGTGATGTCATATGCCATGGAGAAAGGAGTGTCATCAAGGAAGGCTACAAGAGCTTCCCAAGTGGGCATTCTTCAG

upper sequence: GRMZM2G447433_T08 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g27040.1 (Oryza sativa), 3'ss of exon 5
gtaaa-tccttccatcagtgtcatttttc----tttgcaagttcatacctgttg-aacctgtagccactaaatcagatattt-gttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT
||||  |||||     |||||| |  |      | |  || |||||      || |   | ||   |   ||  |    |||  || | ||||| ||| ||||| | || ||  |||| ||||||||||||||||||||||| ||||||||||| || ||||| || |||||||||||||||||||
gtaatctccttgtgctagtgtcctgatctcagatattaaacttcatgtagtctgcaggttatattgaagtaacaaatcgtttcatttttcagAAGTTTGATAATGTCACTACAAATGTCATATGCCATGGAGAAAAGAGTGTTATCAAGGAAGGCCACAAGAGCTTTCCAAGTGGGCATTCTTCAT

upper sequence: GRMZM2G447433_T08 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------gtaaatccttccatcagtgtc-atttttctttgcaagttcatacctgttgaa-cctgtagccactaaatcagatatttg---------ttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT
                              |   |  | |||  | |||  | || | |||     ||  | | || | |  ||| ||  ||   || || |||||||         |||| |||   ||| | | || ||| || |||||  | ||   |||||| || ||||||||||||||||| ||||| |||||||| ||||||||| |||| |
gtgggctctccattacatcaactatctttatttttgttcccaagattgttgacttctgtttatttttttgttcttgatcagtcctatactcagccaa-catatatttggtgcatggattattcagGTGTTTGACACTAGAACAACAGATGTTCTGTGTACTGGAGACAAAAGTGTCATCAAGGAAGGACATAAAAGTTTCCCTAGTGGGCATACTTCTT

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|211211372|gb|FL470796.1|FL470796
EST:     GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCT                         AATTTTAATCATATAACCACCGACGTGATATCCCATGGAGAAAAGAGTGTC
genomic: GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCTgtaaatcctt ... tgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC
EST: gi|211272973|gb|FL366561.1|FL366561
EST:     GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCT                         AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC
genomic: GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCTgtaaatcctt ... tgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC
EST: gi|10697618|gb|BE997342.1|BE997342
EST:     GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCT                         AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC
genomic: GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCTgtaaatcctt ... tgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC
EST: gi|32932160|gb|CF036972.1|CF036972
EST:     GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCT                         AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC
genomic: GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCTgtaaatcctt ... tgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC
EST: gi|71439499|gb|DR820549.1|DR820549
EST:     GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCT                         AATTTTTATAATATAACCACCGATGTGATATGCCATGG
genomic: GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCTgtaaatcctt ... tgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGG
EST: gi|32932582|gb|CF037394.1|CF037394
EST:     GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCT                         AATTTTAATAATATAACCACCGATGCGATATGCCATGGAGAAAAGAGTGTC
genomic: GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCTgtaaatcctt ... tgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC
EST: gi|78114830|gb|DV533218.1|DV533218
EST:     GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCT                         AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC
genomic: GTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGATGGCAAACCTgtaaatcctt ... tgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaagttcatacctgttgaacctgtagccactaaatcagatatttgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT
                             cactaaa  putative branch site (score: 2)
                                taaatcagatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatccttccatcagtgtcatttttctttgcaagttcatacctgttgaacctgtagccactaaatcagatatttgttatccagAATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT

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