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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttattacctttgttttgatgatacttgatactactattagtcactcatctgcagcttgctaacctgactgatcagaagtttttctttttcttttttcagACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGTTCCAAGTTTGGTGCAGTGAAGCATATTTTTGTTGACAAGTAAGCTTTCC

Basic information

species Zea mays
transcript GRMZM2G076597_T05
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076597_T05 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g30370.2 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------------------cttattacctttgttttgatgatacttgatactactattagtcactcatctgca-gcttgctaacctgactgatcagaagtttttctttttcttttttcagACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGTTCCAAGTTTGGTGCAGTGAAGCATATTTTTGTTGACAAGTAAGCTTTCC
                                                                    |||||   |   |    ||| || ||| |  || | | |||   |||  || |    | |  | ||||| ||  |    ||     ||   ||||  |||||||||||||||||||| |||||||||  |||||||||||| ||||| || || |||||||||||||| || || ||||||||||||||           
gtatttatatatttatgttttagtttatcgctctgttccttcaatttagatggccactttacatttctttattgtatgattcaaaatgttatttgtt-ttagtttcagttcatcaattgtatatgttcgcatctgaccgactaa---ttgaatgttcatttttaacagACAGATCCTGATTTTGATTTGGATATTAAAGATGATGTCCAGGATGAATGCTCAAAGTTTGGTGCAGTAAATCACATTTTTGTTGACAA-----------

upper sequence: GRMZM2G076597_T05 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA08G15370.2 (Glycine max), 3'ss of exon 10
cttattacctttgttttgatgatacttgat--actactattagtcactcatctgcagcttgctaacctgactgatcagaagtttttctttttcttttttcagACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGTTCCAAGTTTGGTGCAGTGAAGCATATTTTTGTTGACAAGTAAGCTTTCC
                      | | || |  |||  |  ||  |   ||||    | ||  |||  | ||  || ||   |        ||    |  ||||| || |||||||||||  | || |||  ||| |||||  | || |||||||| || | |||    ||||||||||||||||||||||||||||||| | 
---------------------gtccgtggttaactgattatatacttccatcatatgatttttaatttaacaaattagtgatagcaaacattgcaatg-cagACGGAACCTGATTTTGATATAGACATTAAAGAGGATGTAGAGGAAGAGTGTTCTAAATATGGCCGGGTGAAGCATATTTTTGTTGACAAGTAAGCTTACA

upper sequence: GRMZM2G076597_T05 (Zea mays), 3'ss of exon 10
lower sequence: PP1S207_105V6.1 (Physcomitrella patens), 3'ss of exon 10
--cttattacctttgttttgatgatacttgatactactattagtcactcatctgcagcttgctaacctgact--gatcagaagtttttctttttcttttttcagACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGTTCCAAGTTTGGTGCAGTGAAGCATATTTTTGTTGACAAGTAAGCTTTCC
  ||   |   | ||| |      || ||| |  |  ||    | |   |||   || || ||||  | |    ||  |  | | | |  || || |    ||| | || || ||||||||| |||||||    ||||| || ||||| ||||| || ||||||||||  ||||||||||| |||||||||||           
aactcggtggttgtgtgtgtcctttaattg-tgttcatagatctgatggatcgataggtttctaaaatcatctcgactaacaatgtgtacttgtcat---gcagTCCGACCCGGATTTTGACATGGATATCAAGGATGACGTACAAGAGGAGTGCTCAAAGTTTGGTGTTGTGAAGCATATCTTTGTTGACAA-----------

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|9461704|gb|BE453863.1|BE453863
EST:     CACCTACAGAATTCTTGGTGCTTAAAAACATGTTTGACCCAGCATTGGAG                         ACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGT
genomic: CACCTACAGAATTCTTGTTGCTTAAAAACATGTTTGACCCAGCATTGGAGgtattcctct ... cttttttcagACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGT
EST: gi|9731387|gb|BE510139.1|BE510139
EST:     CACCTACAGAATTCTTGTTGCTTAAAAACATGTTTGACCCAGCATTGGAG                         ACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGT
genomic: CACCTACAGAATTCTTGTTGCTTAAAAACATGTTTGACCCAGCATTGGAGgtattcctct ... cttttttcagACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGT
EST: gi|18661768|gb|BM501569.1|BM501569
EST:     CACCTACAGAATTCTTGTTGCTTAAAAACATGTTTGGCCCAGCATTGGAG                         ACAGATCCTGATTTTGGCTTGGATATTCGAGATGATGTCCAAGATGAGTGT
genomic: CACCTACAGAATTCTTGTTGCTTAAAAACATGTTTGACCCAGCATTGGAGgtattcctct ... cttttttcagACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatctgcagcttgctaacctgactgatcagaagtttttctttttcttttttcagACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGTTCCAAGTTTGGTGCAGTGAAGCATATTTTTGTTGACAAGTAAGCTTTCC
                                  tttttctttttctttt  CT-rich tract
                               aagtttttctttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttattacctttgttttgatgatacttgatactactattagtcactcatctgcagcttgctaacctgactgatcagaagtttttctttttcttttttcagACAGATCCTGATTTTGACTTGGATATTCGAGATGATGTCCAAGATGAGTGTTCCAAGTTTGGTGCAGTGAAGCATATTTTTGTTGACAAGTAAGCTTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - tgatgat
- - - - - - - - - -tgatact
- - - - - - - - - - - - - - - - - - - - - - - - -ctgcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgactg