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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattacttatgcatcaattcagtccagtttctttttaacttaactaattttggatgaacaataatgcgattttataatgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAG

Basic information

species Vitis vinifera
transcript Vv14s0060g01290.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 4
gtaatt-acttatgcatcaattcagtccagtttctttttaacttaactaattttggatgaacaataatgcgattttataatgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAG
||| || | ||| | | || | | | ||| | | || ||| ||| | | | ||| | ||||| |||||| || || |||||||| ||||||||||||||||| ||||| || ||||||| |||
gtattttgcatattcctagctttcttggaatgccttgcttttgtgtct---cttgaatg-----ttaagatattaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 4
--gtaattacttatgcatcaattcagtccagtttctttttaacttaactaattttggatgaacaataatgcgattt-tataatgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAG
|| | | ||| || ||| | ||||| ||| || | || || | | | || | ||| | | |||| |||||||| || |||||||| ||||||||||||||||| ||||| || |||||||||||
gtgtgaagagtta-atatttatt--attgtgtttcaatttc-tttgtttgcacctgtttggagataattgaggtttatgtgttgattgcagCCTGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCAGAG

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 4
gtaattacttatgcatcaattcagtccagtttctttttaacttaactaattttggatgaacaataatgcgattttataatgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAG
|| | ||| || || ||| | |||||||| | ||| ||| || | | | || | | ||||| ||||||| || |||||||| ||||| ||||||||||| ||||| || |||||||||||
gtgaatacata-atatttattgttgtgaatttcttttc--ttgaacctgtttgtaataattgaggttt--atgtgttgatgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 4
gtaattacttatgcatcaattcagtccagtt-tctttttaacttaactaattttggatg-aacaataatgcgattttataatgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAG
||| || | || | ||| | || || || || | ||| || | | || |||| || | |||||| |||||||||||||| || || || |||||||||||||| ||| |||| ||||||
gtacttttcttcccagagttgtagtttaattgtcagatttggtt--ttggtttcggttttgatcatttctaatctttaatatactcacagCCAGAAGATTGGGATGACAAAGAATATATTCCTGATCCTGAGGATAAGAAACCAGAG

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|33401772|gb|CF207399.1|CF207399
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110732858|gb|EE108510.1|EE108510
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAAGATCCTGAGGCCAAGAAA                         ACTGAAGAATTGGGATGAGAAGGAGTACATTCCTGATTCTGAAGATGANNA
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGA-TTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAA
EST: gi|110381806|gb|EC935430.1|EC935430
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110372400|gb|EC936562.1|EC936562
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|351056636|gb|FQ443263.1|FQ443263
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|349816036|gb|FQ413550.1|FQ413550
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|351027478|gb|FQ444727.1|FQ444727
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110700083|gb|EE077719.1|EE077719
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110687770|gb|EE065562.1|EE065562
EST:     ATTGGGATATTCTCCCTCCAAAGAAGA-CAAGGATCCTGAGGCCAAGAAA                         ACTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|349808465|gb|FQ405609.1|FQ405609
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110699525|gb|EE076601.1|EE076601
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110732288|gb|EE107443.1|EE107443
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAAGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|352794106|gb|FQ479348.1|FQ479348
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|349826885|gb|FQ418976.1|FQ418976
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|29781779|gb|CB346544.2|CB346544
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|33401998|gb|CF207625.1|CF207625
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110687446|gb|EE064865.1|EE064865
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|30295872|gb|CB972666.1|CB972666
EST:     ATTGGGATATTTTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110729565|gb|EE105649.1|EE105649
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110357396|gb|EC920905.1|EC920905
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|294964759|gb|GW838562.1|GW838562
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110702773|gb|EE079035.1|EE079035
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTNGA-GATGAGAA
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCT-GAAGATGAGAA
EST: gi|351043138|gb|FQ451311.1|FQ451311
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110688081|gb|EE066225.1|EE066225
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGANGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAAGA-
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGA-GAA
EST: gi|351022735|gb|FQ428644.1|FQ428644
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|33402080|gb|CF207707.1|CF207707
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|77578221|gb|DV217893.1|DV217893
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110727891|gb|EE105170.1|EE105170
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGGAGGAGTACATTCCTGATCCTGAAGATGAGA-G
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|30295943|gb|CB972737.1|CB972737
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|110708716|gb|EE086573.1|EE086573
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|161716555|gb|FC065240.1|FC065240
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|71870544|gb|DT019599.1|DT019599
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
EST: gi|349810157|gb|FQ401603.1|FQ401603
EST:     ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAA                         CCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG
genomic: ATTGGGATATTCTCCCTCCAAAGAAGATCAAGGATCCTGAGGCCAAGAAAgtaattactt ... atgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaacttaactaattttggatgaacaataatgcgattttataatgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAG
          aactaat  putative branch site (score: 2)
 attttataatgataac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattacttatgcatcaattcagtccagtttctttttaacttaactaattttggatgaacaataatgcgattttataatgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC