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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcaaactgctctacctgtgtacactgtacatatctccttgtgacctagactacttattaccaatatatattggctagtcaattctattacttttggatatctattaaattagaaaacaatcttttcccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAGTGCGAGAAAGCTGTCCAAAAGATCCGTTTTGAAGAAGCAATATCTGCTG

Basic information

species Zea mays
transcript GRMZM2G126435_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------gttagcaaactgctctacctgtgtacactgtacatatctccttgtgac---ctagactacttattaccaatatatattggctagtc--aattctattacttttggatatctattaaattagaaaacaatcttttc---ccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAGTGCGAGAAAGCTGTCCAAAAGATCCGTTTTGAAGAAGCAATATCTGCTG
                                               | | |  ||   || |  ||    ||  |       | || | |||      || | || |  |    |  || ||  || |||    ||    |||| |||     || |  || ||||  ||     ||||||   | |||| |||| |||| |||| ||||||||||||||||| || || ||||||||||| |||||||||||||| || |||||||||||||| ||||| ||||  |
gtgcgcagtttgttttcctagttttgtggtctcttcccagattgagtgattgagaatgactatttctagtcacttttcttgcttttcttggtgctgctttatattaatgttggtgaccatctag-ggatagcaggaaccacattattttgtttcatgtggtacattaataagtctacttttctttctagGTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAGTGTGAGAAAGCTGTCCAGAAAATCCGTTTTGAAGAGGCAATTTCTGTAG
















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|32935326|gb|CF040138.1|CF040138
EST:     CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAG                         GTTNNNNNNNTCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
genomic: CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAGgttagcaaac ... cttttcccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
EST: gi|71769984|gb|DR967921.1|DR967921
EST:     CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAG                         GTTNNNNNNNTCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
genomic: CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAGgttagcaaac ... cttttcccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
EST: gi|71436892|gb|DR817942.1|DR817942
EST:     CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAG                         GTTNNNNNNNTCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
genomic: CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAGgttagcaaac ... cttttcccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
EST: gi|60359346|gb|DN226319.1|DN226319
EST:     CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAG                         GTTNNNNNNNTCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
genomic: CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAGgttagcaaac ... cttttcccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
EST: gi|33093738|gb|CF053732.1|CF053732
EST:     CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAG                         GTTNNNNNNNTCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
genomic: CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAGgttagcaaac ... cttttcccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
EST: gi|93012246|gb|EB637766.1|EB637766
EST:     CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAG                         GTTNNNNNNNTCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG
genomic: CTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAGgttagcaaac ... cttttcccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcaattctattacttttggatatctattaaattagaaaacaatcttttcccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAGTGCGAGAAAGCTGTCCAAAAGATCCGTTTTGAAGAAGCAATATCTGCTG
                                            tcttttccc  CT-rich tract
                     atatctattaaattag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcaaactgctctacctgtgtacactgtacatatctccttgtgacctagactacttattaccaatatatattggctagtcaattctattacttttggatatctattaaattagaaaacaatcttttcccagGTTAAAAAAATCTGCCCAAATGATCCAGATGCTACAAGAAAGTTGAAAGAGTGCGAGAAAGCTGTCCAAAAGATCCGTTTTGAAGAAGCAATATCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA