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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGAGGAGCTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgcttactttgtgtatggcctatagttgtagttattttgctttatggttgtccactaaatctgacttttcgctctgcttag

Basic information

species Zea mays
transcript GRMZM2G013750_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 9
GGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGAGGAGCTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgcttactttg-tgtatggcctatagttgtagttattttgctttatggttgtccactaaat-ctgacttttcgctct-gcttag
|||||||| |||  | |||| ||  || ||||||||| | || |||||||||||||||| |||||||||||| ||| ||||  | || || |||||||||||| |||||||||   | ||| |  | |   | | | |   ||||||| |  |||||   | | | |    | || ||| | | | ||
GGAATTCTTTAAAGATGAATATGCGAATGAGAAGAATTTTCTCGGAGGAGCTTTGGGTGACAAAGCTGCAGAGGATCTGAAATTGAGGATCATTGAACATgtattgcttacttgactttatcgtatttctcttttggttccttgctttgtatttgtcagttgatttccagttctttgcttttgttcag

upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 9
--GGAATTC-TCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGAGGAGCTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgta-----ctgcttactttgtgtatg-----gcctatagttgtagttattttgctttatg-gttgtccactaaatctgacttttcgctctgcttag-------------------------------
  || || | | ||||   || ||||| || ||||||   |  || |||  | |||||||||  ||||| ||||||||| ||| || |||||||||||||||||||     ||| |  | || | | |       || ||   | | |||  || |  || |  | | | |  ||  | | |   |||  | ||   |                                
ATGGGATACATATAAGAGTGATTTTGAGAATGAGAAGG--CCTCTGGGAA-ATCTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACATgtaaataactgatgccattatatttcttctcacccatcaattttgttggttggtattgtatgatatgctttatgttttatacttctttttgtgaacattaatatggagcatttttgttacctttcag

upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 9
GGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGAGGAGCTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgcttactt-tgtgtatggcctatagttgtagttattttgctt-tatggttgtccactaaatctg-acttttcgctctgcttag---------------
| |  | | |||| | ||||||||||||||||||||  |||| || ||  | ||||||| |||||||||||||||| | |  |  |||||||||||||||||| || ||   | |   | | |          || || ||||| |  | ||  | |  | | | |  | | || |   | |||  |                
GAATATGTTTAAGGATGAATTTGAAAACGAGAAGAACATGCTTGGGGGCTCCTTGGGTGACAAAGCTGCAGAAGATCTAAGACAGAGAATAATTGAACATgtagtgtttctctgtacatttagttccatacaataatttttttgatcatttgagttttgagttattgggtaattatttgtatgcaaaactgtcttcttttcag

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|60345832|gb|DN212805.1|DN212805
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|60349290|gb|DN216263.1|DN216263
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGT
EST: gi|60344063|gb|DN211036.1|DN211036
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|60358924|gb|DN225897.1|DN225897
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|6031286|gb|AW076143.1|AW076143
EST:     CTNTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|67021450|gb|CO450199.1|CO450199
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|33095588|gb|CF055582.1|CF055582
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGAGGAGCTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgcttactttgtgtatggcctatagttgtagttattttgctttatggttgtccactaaatctgacttttcgctctgcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC