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It is complex. All Junior Village Clubs in Sydney are affiliated with Sydney JRU.
For Representative Rugby purposes, they are all grouped under into geographically based Districts, which conveniently happen to correlate to the Shute Shield Clubs.
Most of the Junior Village Clubs are stand alone Incorporated Entities, and are not answerable to a NSW Suburban Rugby Club Entity, or a Shute Shield Rugby Club Entity. There is often fierce local rivalry between Junior Village Clubs within a District.
Some of the teams playing under the SJRU banner are the "junior division" of a NSW Suburban Rugby Club, such as Oatley, and Newport.
Not many Shute Shield Clubs have an "Junior Division" that plays in SJRU competitions. West Harbour (Shute Shield Club) only has Wests Junior Rugby Club under its wing (although they are in the process of expanding) and they have a thriving Inner West Mini-Rugby Competition going in association with Uni (Shute Shield) and Balmain (Subbies). Most Shute Shield Clubs will have a Junior Rugby SubCommittee established to report to the Main Committee. This SubCommittee is usually made up of Presidents from the Junior Village Clubs in the Area and operates by consensus often with little support or interest from the Senior Club Committee. They typically coordinate the Under 6-Under 9 competitions because SJRU manage Under 10 and above competitions. It can pose some constitutional problems if you want to be pedantic because many of the Junior Village Club Presidents are often not actually registered members of the Shute Shield Club.
Some of the stand alone Junior Village Clubs and District Rep teams get great support from their "parent" Shute Shield District club in terms of moral and financial support, coaching assistance, access to grounds, facilities, junior academies and representative programmes. Others give almost no support apart from allowing the age group rep teams to wear a replica of the club jumper at NSW JRU State Championships.
The only constant is inconsistency.