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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggagtgcttttattctttttttttcttccaatttggatgtgaaaagtcccctattgcttgaataatgcattccttgtgtttccatgctgctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAGAAGAACAGAGTCAGAGGGAAACTGAAATTTAAATCT

Basic information

species Zea mays
transcript GRMZM2G154165_T03
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA16G08410.1 (Glycine max), 3'ss of exon 21
gtggagtgcttttattctttttttttcttccaatttggat-gtgaaaagtcccctattgcttgaataatgcattccttgtgtttccatgctgctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAGAAGAACAGAGTCAGAGGGAAACT---GAAATTTAAATCT
      |   || ||| ||    | | |     ||| ||| |||  |     | |  | | |   ||||  | |   ||| || || | ||  ||  | ||||| |||||||||||||||||| ||||||||||||||||  ||||||| |  ||||||||  |  |||| ||  |    ||||  |||| |
-caacatctgttaattgttaccatgtgtatgtgttttgatagtgttattctgcgttgttccttcctaatctactatgtgt-ttaccttactaatgctttcagGTGTTCACAACTCACCATTGGATGGTTCGGATTTACAAGTTGAAACCACCAAAGAACAGGATTCGAGGAAAGATTAAAAAATCAAAATTT

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 21
gtggagtgcttttattctttttttttcttccaatttggatgtgaaaagtcccctat-tgcttgaataatgcattccttgtgtttccatgctgctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAGAAGAACAGAGTCAGAGGGAAACT---GAAATTTAAATCT
      |  ||| ||| ||    | | |     ||| |||      | ||  || | | | | | ||||  |  || ||||||||| | ||  || || ||||| |||||||||||||||||| ||||||||||||||||  ||||||| |  |||||| |  |  |||| ||  |    ||||  ||||||
actacatcttttaattgttaccatgtgtatgtgttttgatagtgttattctgctttgttccttactaatcta--ccatgtgtttccttactaatgcattcagGTGTTCACAACTCACCATTGGATGGTTCGGATTTACAAGTTGAAACCACCAAAGAACCGGATTCGAGGAAAGATTAAAAAATCAAAATCT

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 19
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 21
gtggagtgcttttattctttttttttcttccaatttggatgtgaaaagtcccctattgcttgaataatgcattccttgtgtttccatgctgctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAGAAGAACAGAGTCAGAGGGAAACT---GAAATTTAAATCT
   | | | ||| | |    | ||| || | ||   || ||     | ||| |||    |    |||    |  || || ||  |||           ||||||||||| | |||||||||| |||||||| | ||||| ||||||||||  | ||||||  |  | || |||     |||| | ||||| 
---gtgagatttaaat----tatttactacaaaccagggtgcattgattccactaggattctggtaa-atgtaactggttttgtcat-----------cagGTTTTCACGAGTCACCATTGGATGGTTCGGCTATACAAGCTGAAACCTCCCAGGAACAGGATTCGTGGTAAAGCAAAGAAACTGAAATCG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 19
lower sequence: Vv03s0088g00210.t01 (Vitis vinifera), 3'ss of exon 7
gtggagtgcttttattctttttttttcttccaatttggatgtgaaaagtcccctattgcttgaataatgcattccttgtgtttccatgctgctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAGAAGAACAGAGTCAGAGGGAAACT---GAAATTTAAATCT
                  | ||| || | || ||          |||||||| | |   ||   | ||  | | |   || ||      |  |  ||  |||| ||||| |||||||||||| |||||||||| |||||| | ||||||| |||||||||  |  | |  ||| |   |||||  ||||| 
-----------------gtctttattttccctat----------aaagtcccatgtctgttc--tgattaacttcccatggttt----ataatcaatgaagGTGTTCACTACTCACCATTGGATGGTTCGGATATACAAATTAAAACCTCCGAAGAACAGGATTCGTGTAAAAATAAAGAAATCAAAATCG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 19
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 21
gtggagtgcttttattctttttttttcttccaatttggatgtgaaaagtc--ccctattgcttgaataatgcattcc--ttgtgtttccatgct----gctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAGAAGAACAGAGTCAGAGGGAAACT---GAAATTTAAATCT
             |  | ||       |   |||||   | |||| | |   ||||||  | |      |   |||   ||   |||||||| |     ||  ||  |||| ||||| |||||||||||| |||||||||| |||||||| || |||| |||||||||  || | |  |||     |||||  ||||| 
---------caccaacccttccgagattaggaattttcgtttgaataattttccctataacgtcccatgtctgttctgattaactttccatggtttatactcaatgaagGTGTTCACTACTCACCATTGGATGGTTCGGATATACAAACTAAAGCCTCCGAAGAACAGGATCCGTGTAAAAACAAAGAAATCAAAATCG

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|67014712|gb|CO443461.1|CO443461
EST:     GAAGATATGAAATAGGGAAGAAACATTTTAAACTTACGCATTTTGAGGAG                         GTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAG
genomic: GAAGATATGAAATAGGGAAGAAACATTTTAAACTTACGCATTTTGAGGAGgtggagtgct ... ctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAG
EST: gi|76017469|gb|DT944639.1|DT944639
EST:     GAAGATATGAAATAGGGAAGAAACATTTTAAACTTACGCATTTTGAGGAG                         GTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAG
genomic: GAAGATATGAAATAGGGAAGAAACATTTTAAACTTACGCATTTTGAGGAGgtggagtgct ... ctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAG
EST: gi|166430326|gb|EG175776.1|EG175776
EST:     GAAGATATGAAATAGGGAAGAAACATTTTAAACTTACGCATTTTGAGGAG                         GTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAG
genomic: GAAGATATGAAATAGGGAAGAAACATTTTAAACTTACGCATTTTGAGGAGgtggagtgct ... ctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcccctattgcttgaataatgcattccttgtgtttccatgctgctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAGAAGAACAGAGTCAGAGGGAAACTGAAATTTAAATCT
             ttgaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggagtgcttttattctttttttttcttccaatttggatgtgaaaagtcccctattgcttgaataatgcattccttgtgtttccatgctgctggatacagGTTTTCACAACTCACCATTGGCTGGTTCGGATTTACAAACTGAAACCTCAGAAGAACAGAGTCAGAGGGAAACTGAAATTTAAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC