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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaatggcagtacctccttgcattcgctgaataatgaacgtgagaagtgcatatatgaactttgtggagcaatcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAGGGGGTTTTGGATCCAAAGATGACTGAGAAGCCTACTTCTAGGGCATTGA

Basic information

species Zea mays
transcript GRMZM2G050861_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050861_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g35080.1 (Oryza sativa), 3'ss of exon 5
gttagtaatggcagtacctccttgcat--tcgctgaataatgaacgtgagaagtgcatatatgaactttgtggagcaatcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAGGGGGTTTTGGATCCAAAGATGACTGAGAAGCCTACTTCTAGGGCATTGA
|||||| || |   | |||  ||  |      || ||| | || | ||   | ||||| |||||| |  |   |  |||| |||||| ||||||| ||||| ||||||||||| ||||| |||||| |||| ||||| ||||||||||||||||||||||||||||||||||||||||||||| |||
gttagttattgtt-tgccttgttataaggattctaaattaagatcttgtcgaatgcatctatgaaatcagcacattaatcctttcagGTTAATCTTGTTGAATGGCTGAAGACAATGGTGAGCAACCGAAACTCTGAAGGGGTTTTGGATCCAAAGATGACTGAGAAGCCTACTTCTAGGGCACTGA

upper sequence: GRMZM2G050861_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------gttagtaatggcagtacctccttgcattcgctgaataatgaac------gtgagaagtgcatat-atgaactttgtggagcaatc-----ttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAGGGGGTTTTGGATCCAAAGATGACTGAGAAGCCTACTTCTAGGGCATTGA
                            || || |||    ||  |   |  | | |||||| | ||  |       ||    ||       ||    |||    |  ||||     ||||||| | ||  ||||||| ||||| |||| |||||| | || ||| ||| | ||||| |||||||||||||||||  |||||||||| ||||| ||||| ||||
gtatgccctaaactacttggatcgtttcttggtgatgatt-tagttatgtaaaat-gctgaagattgtccttttttatgtttggtcttccccattgcttttactcacaaatcaggaattttcagGTGAACTTAGTTGACTGGCTTAAGAGGATGGTTACCAGCAGGAATCCAGAGGGAGTTTTGGATCCAAAGATACCTGAGAAGCCGACTTCAAGGGCCTTGA
















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|32930647|gb|CF035459.1|CF035459
EST:     ACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAA
genomic: ACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|67012855|gb|CO441604.1|CO441604
EST:     AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|6760613|gb|AW324712.1|AW324712
EST:     AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGTAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|71762004|gb|DR959941.1|DR959941
EST:     AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|6742388|gb|AW313203.1|AW313203
EST:     AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGTAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|5555472|gb|AI881423.1|AI881423
EST:     AAATAATATCTGGTCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGGGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|76011103|gb|DT938273.1|DT938273
EST:     AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|50327546|gb|CO522672.1|CO522672
EST:     AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|78179542|gb|DV549915.1|DV549915
EST:     AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGTAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|78087662|gb|DV516055.1|DV516055
EST:     AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
EST: gi|67010388|gb|CO439137.1|CO439137
EST:     AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAG                         ATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG
genomic: AAATAATATCTGGCCGTGTACCTGTTGATTACAACAGGCCGCCAGGGGAGgttagtaatg ... atcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaataatgaacgtgagaagtgcatatatgaactttgtggagcaatcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAGGGGGTTTTGGATCCAAAGATGACTGAGAAGCCTACTTCTAGGGCATTGA
                                              tcttttc  CT-rich tract
                        atatatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaatggcagtacctccttgcattcgctgaataatgaacgtgagaagtgcatatatgaactttgtggagcaatcttttcagATTAATCTAGTTGAGTGGCTGAAGACGATGGTCAGCAACAGAAATTCTGAGGGGGTTTTGGATCCAAAGATGACTGAGAAGCCTACTTCTAGGGCATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC